From a7c97250a135c656fc70ff047103027a074e36ca Mon Sep 17 00:00:00 2001 From: Eric Kofman Date: Mon, 15 Jul 2024 16:16:27 -0700 Subject: [PATCH] enable auto-generation of bedgraphs --- .../final_filtered_site_info.tsv | 5804 ++++++++--------- .../final_filtered_site_info.tsv | 2422 +++---- examples/test_bulk_subset_AI.sh | 2 +- examples/test_bulk_subset_CT.sh | 2 +- marine.py | 67 +- tests/integration_tests.ipynb | 2493 +------ .../scripts/unstranded_pair_test.sh | 2 +- .../final_filtered_site_info.tsv | 16 +- 8 files changed, 4209 insertions(+), 6599 deletions(-) diff --git a/examples/bulk_subset_AI/final_filtered_site_info.tsv b/examples/bulk_subset_AI/final_filtered_site_info.tsv index ef072f2..f7b31e5 100644 --- a/examples/bulk_subset_AI/final_filtered_site_info.tsv +++ b/examples/bulk_subset_AI/final_filtered_site_info.tsv @@ -1,2984 +1,2984 @@ site_id barcode contig position ref alt strand count coverage conversion strand_conversion -no_barcode_1_150623676_T_C_- no_barcode 1 150623676 T C - 1 1 T>C A>G -no_barcode_1_35184462_T_C_- no_barcode 1 35184462 T C - 1 3 T>C A>G -no_barcode_1_86354584_C_T_- no_barcode 1 86354584 C T - 1 1 C>T G>A -no_barcode_1_200409192_C_A_- no_barcode 1 200409192 C A - 1 1 C>A G>T -no_barcode_1_180495507_T_C_- no_barcode 1 180495507 T C - 1 1 T>C A>G -no_barcode_1_32334030_T_C_- no_barcode 1 32334030 T C - 1 7 T>C A>G -no_barcode_1_16445023_A_G_+ no_barcode 1 16445023 A G + 1 1 A>G A>G -no_barcode_1_16620448_T_C_- no_barcode 1 16620448 T C - 1 1 T>C A>G -no_barcode_1_1703421_G_T_- no_barcode 1 1703421 G T - 1 1 G>T C>A -no_barcode_1_8863310_G_T_- no_barcode 1 8863310 G T - 1 35 G>T C>A -no_barcode_1_1387212_C_G_- no_barcode 1 1387212 C G - 1 4 C>G G>C -no_barcode_1_206696189_T_C_- no_barcode 1 206696189 T C - 1 7 T>C A>G -no_barcode_1_43993797_A_G_+ no_barcode 1 43993797 A G + 1 1 A>G A>G -no_barcode_1_9729137_T_C_- no_barcode 1 9729137 T C - 1 2 T>C A>G -no_barcode_1_32333901_T_C_- no_barcode 1 32333901 T C - 1 3 T>C A>G -no_barcode_1_77210439_A_C_- no_barcode 1 77210439 A C - 1 1 A>C T>G -no_barcode_1_151248584_A_T_+ no_barcode 1 151248584 A T + 1 2 A>T A>T -no_barcode_1_1477854_C_T_+ no_barcode 1 1477854 C T + 1 1 C>T C>T -no_barcode_1_155965739_C_G_- no_barcode 1 155965739 C G - 1 1 C>G G>C -no_barcode_1_161323679_C_T_+ no_barcode 1 161323679 C T + 1 1 C>T C>T -no_barcode_1_46132121_C_G_- no_barcode 1 46132121 C G - 1 1 C>G G>C -no_barcode_1_630015_T_C_+ no_barcode 1 630015 T C + 1 8 T>C T>C -no_barcode_1_156055305_C_T_+ no_barcode 1 156055305 C T + 3 4 C>T C>T -no_barcode_1_228098437_A_G_+ no_barcode 1 228098437 A G + 1 9 A>G A>G -no_barcode_1_185963783_A_G_+ no_barcode 1 185963783 A G + 1 1 A>G A>G -no_barcode_1_151983123_G_A_- no_barcode 1 151983123 G A - 1 3 G>A C>T -no_barcode_1_202893362_T_C_- no_barcode 1 202893362 T C - 1 1 T>C A>G -no_barcode_1_205715670_T_C_- no_barcode 1 205715670 T C - 1 4 T>C A>G -no_barcode_1_32334027_T_C_- no_barcode 1 32334027 T C - 1 8 T>C A>G -no_barcode_1_152032715_T_C_- no_barcode 1 152032715 T C - 1 2 T>C A>G -no_barcode_1_182859086_A_G_+ no_barcode 1 182859086 A G + 1 1 A>G A>G -no_barcode_1_22086683_A_G_+ no_barcode 1 22086683 A G + 1 3 A>G A>G -no_barcode_1_207794374_T_C_+ no_barcode 1 207794374 T C + 1 1 T>C T>C -no_barcode_1_25223391_T_C_- no_barcode 1 25223391 T C - 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1 1 T>C A>G -no_barcode_1_220147698_A_G_+ no_barcode 1 220147698 A G + 1 2 A>G A>G -no_barcode_1_161362718_G_T_+ no_barcode 1 161362718 G T + 1 1 G>T G>T -no_barcode_1_68159177_T_C_- no_barcode 1 68159177 T C - 1 2 T>C A>G -no_barcode_1_33013329_T_C_- no_barcode 1 33013329 T C - 1 8 T>C A>G -no_barcode_1_15660316_A_G_+ no_barcode 1 15660316 A G + 1 1 A>G A>G -no_barcode_1_36303445_G_T_+ no_barcode 1 36303445 G T + 1 1 G>T G>T -no_barcode_1_42701014_A_G_+ no_barcode 1 42701014 A G + 1 15 A>G A>G -no_barcode_1_235437396_A_T_+ no_barcode 1 235437396 A T + 1 1 A>T A>T -no_barcode_1_64666063_C_T_+ no_barcode 1 64666063 C T + 1 1 C>T C>T -no_barcode_1_236226306_T_C_- no_barcode 1 236226306 T C - 1 1 T>C A>G -no_barcode_1_154157532_T_C_- no_barcode 1 154157532 T C - 1 2 T>C A>G -no_barcode_1_175945048_T_C_- no_barcode 1 175945048 T C - 1 1 T>C A>G -no_barcode_1_37860816_T_C_- no_barcode 1 37860816 T C - 1 1 T>C A>G -no_barcode_1_112912753_T_C_- no_barcode 1 112912753 T C - 1 1 T>C A>G -no_barcode_1_154551806_C_G_- no_barcode 1 154551806 C G - 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1 8 A>G T>C diff --git a/examples/bulk_subset_CT/final_filtered_site_info.tsv b/examples/bulk_subset_CT/final_filtered_site_info.tsv index 049deae..0240f5f 100644 --- a/examples/bulk_subset_CT/final_filtered_site_info.tsv +++ b/examples/bulk_subset_CT/final_filtered_site_info.tsv @@ -1,1273 +1,1273 @@ site_id barcode contig position ref alt strand count coverage conversion strand_conversion -no_barcode_1_204520137_C_A_- no_barcode 1 204520137 C A - 1 1 C>A G>T -no_barcode_1_68159190_G_A_- no_barcode 1 68159190 G A - 1 1 G>A C>T -no_barcode_1_154582824_G_T_- no_barcode 1 154582824 G T - 1 1 G>T C>A +no_barcode_1_151266575_T_C_+ no_barcode 1 151266575 T C + 3 3 T>C T>C +no_barcode_1_171592086_C_T_+ no_barcode 1 171592086 C T + 1 1 C>T C>T +no_barcode_1_175000171_C_T_+ no_barcode 1 175000171 C T + 1 1 C>T C>T +no_barcode_1_634848_A_C_+ no_barcode 1 634848 A C + 1 30 A>C A>C +no_barcode_1_171704096_G_A_- no_barcode 1 171704096 G A - 1 1 G>A C>T +no_barcode_1_91049666_C_A_+ no_barcode 1 91049666 C A + 3 3 C>A C>A +no_barcode_1_38839056_A_G_- no_barcode 1 38839056 A G - 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1 16 T>A A>T +no_barcode_1_30941233_G_A_- no_barcode 1 30941233 G A - 1 1 G>A C>T +no_barcode_1_944307_T_C_+ no_barcode 1 944307 T C + 1 2 T>C T>C +no_barcode_1_226361534_C_A_- no_barcode 1 226361534 C A - 1 3 C>A G>T +no_barcode_1_28203811_C_A_+ no_barcode 1 28203811 C A + 1 4 C>A C>A +no_barcode_1_37540158_G_A_- no_barcode 1 37540158 G A - 1 1 G>A C>T +no_barcode_1_234393445_C_T_+ no_barcode 1 234393445 C T + 1 2 C>T C>T +no_barcode_1_202728943_G_A_- no_barcode 1 202728943 G A - 1 1 G>A C>T +no_barcode_1_71070920_T_A_- no_barcode 1 71070920 T A - 1 1 T>A A>T +no_barcode_1_1586962_C_T_- no_barcode 1 1586962 C T - 1 1 C>T G>A +no_barcode_1_228100806_G_A_- no_barcode 1 228100806 G A - 1 2 G>A C>T +no_barcode_1_24157001_A_G_- no_barcode 1 24157001 A G - 1 1 A>G T>C +no_barcode_1_62454150_A_G_+ no_barcode 1 62454150 A G + 1 1 A>G A>G +no_barcode_1_114727027_C_G_- no_barcode 1 114727027 C G - 1 5 C>G G>C +no_barcode_1_16992098_G_A_- no_barcode 1 16992098 G A - 1 2 G>A C>T +no_barcode_1_201464814_G_T_- no_barcode 1 201464814 G T - 1 1 G>T C>A +no_barcode_1_160277395_G_C_- no_barcode 1 160277395 G C - 1 1 G>C C>G +no_barcode_1_173859748_A_G_+ no_barcode 1 173859748 A G + 1 2 A>G A>G +no_barcode_1_111766331_T_C_+ no_barcode 1 111766331 T C + 2 2 T>C T>C +no_barcode_1_150235748_G_C_- no_barcode 1 150235748 G C - 1 2 G>C C>G +no_barcode_1_225920175_A_T_- no_barcode 1 225920175 A T - 1 3 A>T T>A +no_barcode_1_23507204_G_A_- no_barcode 1 23507204 G A - 1 1 G>A C>T diff --git a/examples/test_bulk_subset_AI.sh b/examples/test_bulk_subset_AI.sh index b33b187..69bebe3 100644 --- a/examples/test_bulk_subset_AI.sh +++ b/examples/test_bulk_subset_AI.sh @@ -1,3 +1,3 @@ #! /bin/bash -marine.py --bam_filepath $MARINE/examples/data/bulk_AI.md.subset.bam --output_folder $MARINE/examples/bulk_subset_AI --strandedness 2 --cores 16 --annotation_bedfile_path $MARINE/annotations/hg38_gencode.v35.annotation.genes.bed --contigs "1" \ No newline at end of file +marine.py --bam_filepath $MARINE/examples/data/bulk_AI.md.subset.bam --output_folder $MARINE/examples/bulk_subset_AI --strandedness 2 --cores 16 --annotation_bedfile_path $MARINE/annotations/hg38_gencode.v35.annotation.genes.bed --contigs "1" --bedgraphs "AI" \ No newline at end of file diff --git a/examples/test_bulk_subset_CT.sh b/examples/test_bulk_subset_CT.sh index 1242bfe..36c4b73 100644 --- a/examples/test_bulk_subset_CT.sh +++ b/examples/test_bulk_subset_CT.sh @@ -1,3 +1,3 @@ #! /bin/bash -marine.py --bam_filepath $MARINE/examples/data/bulk_CT.md.subset.bam --output_folder $MARINE/examples/bulk_subset_CT --strandedness 2 --cores 16 --annotation_bedfile_path $MARINE/annotations/hg38_gencode.v35.annotation.genes.bed --contigs "1" \ No newline at end of file +marine.py --bam_filepath $MARINE/examples/data/bulk_CT.md.subset.bam --output_folder $MARINE/examples/bulk_subset_CT --strandedness 2 --cores 16 --annotation_bedfile_path $MARINE/annotations/hg38_gencode.v35.annotation.genes.bed --contigs "1" --bedgraphs "CT" \ No newline at end of file diff --git a/marine.py b/marine.py index 5055149..498223c 100755 --- a/marine.py +++ b/marine.py @@ -41,10 +41,11 @@ def delete_intermediate_files(output_folder): for object in to_delete: object_path = '{}/{}'.format(output_folder, object) - if os.path.isfile(object_path): - os.remove(object_path) - else: - shutil.rmtree(object_path) + if os.path.exists(object_path): + if os.path.isfile(object_path): + os.remove(object_path) + else: + shutil.rmtree(object_path) def edit_finder(bam_filepath, output_folder, strandedness, barcode_tag="CB", barcode_whitelist=None, contigs=[], num_intervals_per_contig=16, @@ -249,12 +250,20 @@ def collate_edit_info_shards(output_folder): print("\tColumns of collated edit info df: {}".format(collated_df.columns)) return collated_df -def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_intervals_per_contig=16, strandedness=True, barcode_tag="CB", paired_end=False, barcode_whitelist_file=None, verbose=False, coverage_only=False, filtering_only=False, annotation_only=False, sailor=False, min_base_quality = 15, min_read_quality = 0, min_dist_from_end = 10, max_edits_per_read = None, cores = 64, number_of_expected_bams=4, +def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_intervals_per_contig=16, strandedness=True, barcode_tag="CB", paired_end=False, barcode_whitelist_file=None, verbose=False, coverage_only=False, filtering_only=False, annotation_only=False, bedgraphs_list=[], sailor=False, min_base_quality = 15, min_read_quality = 0, min_dist_from_end = 10, max_edits_per_read = None, cores = 64, number_of_expected_bams=4, keep_intermediate_files=False, skip_coverage=False): print_marine_logo() + # Check to make sure the folder is empty, otherwise prompt for overwriting + # Getting the list of directories + dir = os.listdir(output_folder) + + # Checking if the list is empty or not + if len(dir) > 0: + pretty_print("WARNING {} is not empty".format(output_folder), style="^") + logging_folder = "{}/metadata".format(output_folder) make_folder(logging_folder) @@ -339,10 +348,7 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in pretty_print("Total time to calculate coverage: {} minutes".format(round(total_time/60, 3))) - #all_edit_info_pd = pd.concat(results) - #if verbose: - # all_edit_info_pd.to_csv('{}/all_edit_info.tsv'.format(output_folder), sep='\t') # Filtering and site-level information # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -355,12 +361,7 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in names=['barcode', 'contig', 'position', 'ref', 'alt', 'read_id', 'strand', 'dist_from_end', 'base_quality', 'mapping_quality', 'barcode_position', 'coverage', 'source', 'position_barcode'], dtype={'base_quality': int, 'dist_from_end': int, 'contig': str}) - - #all_edit_info_pd['contig'] = all_edit_info_pd['contig'].astype(str) - - # Ensure that we are taking cleaning for only unique edits - # TODO fix thisssssss - #all_edit_info_pd['position_barcode'] = all_edit_info_pd['position'].astype(str) + '_' + all_edit_info_pd['barcode'].astype(str) + coverage_per_unique_position_df = pd.DataFrame(all_edit_info_pd.groupby( [ @@ -493,6 +494,22 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in sep='\t') weird_sites.to_csv('{}/problematic_sites.tsv'.format(output_folder), sep='\t') + + if len(bedgraphs_list) > 0: + # Make plot of edit distributions + bedgraph_folder = '{}/bedgraphs'.format(output_folder) + make_folder(bedgraph_folder) + + pretty_print("Making bedgraphs for {} conversions...\n".format(bedgraphs_list)) + for conversion in bedgraphs_list: + conversion_search = conversion[0] + '>' + conversion[1] + sites_for_conversion = final_site_level_information_df[final_site_level_information_df.conversion == conversion_search] + sites_for_conversion['edit_fraction'] = sites_for_conversion['count']/sites_for_conversion['coverage'] + sites_for_conversion['start'] = sites_for_conversion['position'] - 1 + sites_for_conversion_bedgraph_cols = sites_for_conversion[['contig', 'start', 'position', 'edit_fraction']] + + sites_for_conversion_bedgraph_cols.to_csv('{}/{}_{}.bedgraph'.format(bedgraph_folder, output_folder.split('/')[-1], conversion), sep='\t', index=False, + header=False) if not annotation_bedfile_path: print("annotation_bedfile_path argument not provided ...\ @@ -550,7 +567,7 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in parser.add_argument('--cores', type=int, default=multiprocessing.cpu_count()) - parser.add_argument('--strandedness', type=int, + parser.add_argument('--strandedness', type=int, choices=[0, 1, 2], help='If flag is used, then assume read 2 maps to the sense strand (and read 1 to antisense), otherwise assume read 1 maps to the sense strand') parser.add_argument('--coverage', dest='coverage_only', action='store_true') @@ -566,6 +583,7 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in parser.add_argument('--min_read_quality', type=int, default=0, help='Minimum read quality, default is 0... every aligner assigns mapq scores differently, so double-check the range of qualities in your sample before setting this filter') parser.add_argument('--sailor', dest='sailor', action='store_true') + parser.add_argument('--bedgraphs', type=str, default=None, help='Conversions for which to output a bedgraph for non-single cell runs, e.g. CT, AI') parser.add_argument('--verbose', dest='verbose', action='store_true') parser.add_argument('--keep_intermediate_files', dest='keep_intermediate_files', action='store_true') parser.add_argument('--paired_end', dest='paired_end', action='store_true', help='Assess coverage taking without double-counting paired end overlapping regions... slower but more accurate. Edits by default are only counted once for an entire pair, whether they show up on both ends or not.') @@ -586,7 +604,8 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in coverage_only = args.coverage_only filtering_only = args.filtering_only annotation_only= args.annotation_only - + + bedgraphs = args.bedgraphs sailor = args.sailor verbose = args.verbose keep_intermediate_files = args.keep_intermediate_files @@ -601,6 +620,18 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in num_intervals_per_contig = args.num_intervals_per_contig + # Convert bedgraphs argument into list of conversions + if bedgraphs: + if barcode_tag in ['CB', 'IB']: + sys.stderr.write("Can only output bedgraphs for bulk sequencing runs of MARINE") + sys.exit(1) + + bedgraphs_list = bedgraphs.upper().replace('I', 'G').split(',') + for b in bedgraphs_list: + assert(b in ['AC', 'AG', 'AT', 'CA', 'CG', 'CT', 'GA', 'GC', 'GT', 'TA', 'TC', 'TG']) + else: + bedgraphs_list = [] + assert(strandedness in [0, 1, 2]) if not os.path.exists(output_folder): @@ -626,10 +657,11 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in "\tFiltering only:\t{}".format(filtering_only), "\tAnnotation only:\t{}".format(annotation_only), "\tSailor outputs:\t{}".format(sailor), + "\tBedgraphs:\t{}".format(bedgraphs_list), "\tMinimum base quality:\t{}".format(min_base_quality), "\tMinimum read quality:\t{}".format(min_read_quality), "\tMinimum distance from end:\t{}".format(min_dist_from_end), - "\tmax_edits_per_read:\t{}".format(max_edits_per_read), + "\tMaximum edits per read:\t{}".format(max_edits_per_read), "\tContigs:\t{}".format(contigs), "\tNumber of intervals:\t{}".format(num_intervals_per_contig), "\tCores:\t{}".format(cores), @@ -660,6 +692,7 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in filtering_only=filtering_only, annotation_only=annotation_only, sailor=sailor, + bedgraphs_list=bedgraphs_list, min_base_quality = min_base_quality, min_read_quality = min_read_quality, min_dist_from_end = min_dist_from_end, diff --git a/tests/integration_tests.ipynb b/tests/integration_tests.ipynb index 2f9458e..a5a64dc 100644 --- a/tests/integration_tests.ipynb +++ b/tests/integration_tests.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 3, + "execution_count": 1, "id": "9f2684b1-dbad-45d5-bdb5-b83989bec7dc", "metadata": {}, "outputs": [], @@ -12,7 +12,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 2, "id": "63b5feff-aa8a-417c-8c93-9b9d74e5dee9", "metadata": {}, "outputs": [], @@ -23,7 +23,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 3, "id": "f6012705-9d34-4997-8681-c7bbcc4f008b", "metadata": {}, "outputs": [], @@ -60,7 +60,7 @@ }, { "cell_type": "code", - "execution_count": 26, + "execution_count": 9, "id": "ba12c2b8-2ccb-4866-86c8-a2284fd1229f", "metadata": { "scrolled": true @@ -89,14 +89,16 @@ "\tFiltering only:\tFalse\n", "\tAnnotation only:\tFalse\n", "\tSailor outputs:\tTrue\n", + "\tBedgraphs:\t['CT']\n", "\tMinimum base quality:\t0\n", "\tMinimum read quality:\t0\n", "\tMinimum distance from end:\t0\n", - "\tmax_edits_per_read:\tNone\n", + "\tMaximum edits per read:\tNone\n", "\tContigs:\tall\n", "\tNumber of intervals:\t1\n", "\tCores:\t1\n", "\tVerbose:\tFalse\n", + "\tKeep intermediate files:\tFalse\n", "\tSkip coverage?:\tFalse\n", "\n", ":::: :::: ::: ::::::::: ::::::::::: :::: ::: :::::::::: \n", @@ -116,7 +118,7 @@ "\tContig Citrine.dna\n", "1 total jobs\n", "Reads processed:\t44\n", - "Time to process reads in min:\t0.03751\n", + "Time to process reads in min:\t0.03127\n", "Summary:\t Citrine.dna\n", "edited 25\n", "no_edits 19\n", @@ -133,13 +135,25 @@ "name": "stderr", "output_type": "stream", "text": [ - "100%|██████████| 1/1 [00:02<00:00, 2.20s/it]\n", - "100%|██████████| 1/1 [00:02<00:00, 2.22s/it]\n", - "***** WARNING: File /tmp/pybedtools.ab0mhyn2.tmp has inconsistent naming convention for record:\n", - "Citrine.dna\t436\t438\tno_barcode_Citrine.dna_437_A_G_+\tA>G\t+\n", - "\n", - "***** WARNING: File /tmp/pybedtools.ab0mhyn2.tmp has inconsistent naming convention for record:\n", - "Citrine.dna\t436\t438\tno_barcode_Citrine.dna_437_A_G_+\tA>G\t+\n", + "100%|██████████| 1/1 [00:01<00:00, 1.84s/it]\n", + "100%|██████████| 1/1 [00:01<00:00, 1.90s/it]\n", + "/tscc/projects/ps-yeolab3/ekofman/sailor2//marine.py:498: SettingWithCopyWarning: \n", + "A value is trying to be set on a copy of a slice from a DataFrame.\n", + "Try using .loc[row_indexer,col_indexer] = value instead\n", + "\n", + "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", + " sites_for_conversion['edit_fraction'] = sites_for_conversion['count']/sites_for_conversion['coverage']\n", + "/tscc/projects/ps-yeolab3/ekofman/sailor2//marine.py:499: SettingWithCopyWarning: \n", + "A value is trying to be set on a copy of a slice from a DataFrame.\n", + "Try using .loc[row_indexer,col_indexer] = value instead\n", + "\n", + "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", + " sites_for_conversion['start'] = sites_for_conversion['position'] - 1\n", + "***** WARNING: File /tmp/pybedtools.opv1qqpw.tmp has inconsistent naming convention for record:\n", + "Citrine.dna\t413\t415\tno_barcode_Citrine.dna_414_G_C_+\tG>C\t+\n", + "\n", + "***** WARNING: File /tmp/pybedtools.opv1qqpw.tmp has inconsistent naming convention for record:\n", + "Citrine.dna\t413\t415\tno_barcode_Citrine.dna_414_G_C_+\tG>C\t+\n", "\n" ] }, @@ -149,7 +163,7 @@ "text": [ "Concatenating results...\n", "Done concatenating.\n", - "Total time to calculate coverage: 0.037 minutes\n", + "Total time to calculate coverage: 0.032 minutes\n", "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", "Filtering and calculating site-level statistics\n", "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", @@ -175,2451 +189,14 @@ "14 sites being converted to SAILOR format...\n", "0 rows had coverage of 0 or more edits than coverage... filtering these out, but look into them...\n", "2 final deduplicated SAILOR-formatted sites\n", - "Annotating sites with GTF information from /tscc/projects/ps-yeolab3/ekofman/sailor2//annotations/hg38_gencode.v35.annotation.genes.bed...\n", - "Current memory usage 21.57409MB; Peak: 22.682477MB\n", - "Time elapsed: 5.77s\n", - "++++++\n", - "Done!\n", - "++++++\n", - "F1R2_pair_test-single_end_mode\n", - "Removing old files...\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "rm: cannot remove 'tests/strandedness_tests/F1R2_pair_test-single_end_mode/*': No such file or directory\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Running tests...\n", - "Python is /tscc/nfs/home/ekofman/miniconda3/envs/marine_environment/bin/python\n", - "Assuming 16 cores available for multiprocessing. Set this to the number of available cores for optimal execution.\n", - "Arguments:\n", - "\tBAM filepath:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/bams/F1R2_pair.bam\n", - "\tAnnotation bedfile filepath:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//annotations/hg38_gencode.v35.annotation.genes.bed\n", - "\tOutput folder:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/F1R2_pair_test-single_end_mode\n", - "\tBarcode whitelist:\tNone\n", - "\tStrandedness:\t2\n", - "\tBarcode Tag:\tNone\n", - "\tPaired End:\tFalse\n", - "\tCoverage only:\tFalse\n", - "\tFiltering only:\tFalse\n", - "\tAnnotation only:\tFalse\n", - "\tSailor outputs:\tTrue\n", - "\tMinimum base quality:\t0\n", - "\tMinimum read quality:\t0\n", - "\tMinimum distance from end:\t0\n", - "\tmax_edits_per_read:\tNone\n", - "\tContigs:\tchr17\n", - "\tNumber of intervals:\t16\n", - "\tCores:\t16\n", - "\tVerbose:\tTrue\n", - "\tSkip coverage?:\tFalse\n", - "\n", - ":::: :::: ::: ::::::::: ::::::::::: :::: ::: :::::::::: \n", - "+:+:+: :+:+:+ :+: :+: :+: :+: :+: :+:+: :+: :+: \n", - "+:+ +:+:+ +:+ +:+ +:+ +:+ +:+ +:+ :+:+:+ +:+ +:+ \n", - "+#+ +:+ +#+ +#++:++#++: +#++:++#: +#+ +#+ +:+ +#+ +#++:++# \n", - "+#+ +#+ +#+ +#+ +#+ +#+ +#+ +#+ +#+#+# +#+ \n", - "#+# #+# #+# #+# #+# #+# #+# #+# #+#+# #+# \n", - "### ### ### ### ### ### ########### ### #### ########## \n", - "==================================================================\n", - "Multi-core Algorithm for Rapid Identification of Nucleotide Edits\n", - "==================================================================\n", - "~~~~~~~~~~~~~~~~~~\n", - "Identifying edits\n", - "~~~~~~~~~~~~~~~~~~\n", - "Each contig is being split into 16 subsets...\n", - "contig_lengths_dict:{'chr1': 248956422, 'chr2': 242193529, 'chr3': 198295559, 'chr4': 190214555, 'chr5': 181538259, 'chr6': 170805979, 'chr7': 159345973, 'chr8': 145138636, 'chr9': 138394717, 'chr10': 133797422, 'chr11': 135086622, 'chr12': 133275309, 'chr13': 114364328, 'chr14': 107043718, 'chr15': 101991189, 'chr16': 90338345, 'chr17': 83257441, 'chr18': 80373285, 'chr19': 58617616, 'chr20': 64444167, 'chr21': 46709983, 'chr22': 50818468, 'chrX': 156040895, 'chrY': 57227415, 'chrM': 16569, 'chr1_KI270706v1_random': 175055, 'chr1_KI270707v1_random': 32032, 'chr1_KI270708v1_random': 127682, 'chr1_KI270709v1_random': 66860, 'chr1_KI270710v1_random': 40176, 'chr1_KI270711v1_random': 42210, 'chr1_KI270712v1_random': 176043, 'chr1_KI270713v1_random': 40745, 'chr1_KI270714v1_random': 41717, 'chr2_KI270715v1_random': 161471, 'chr2_KI270716v1_random': 153799, 'chr3_GL000221v1_random': 155397, 'chr4_GL000008v2_random': 209709, 'chr5_GL000208v1_random': 92689, 'chr9_KI270717v1_random': 40062, 'chr9_KI270718v1_random': 38054, 'chr9_KI270719v1_random': 176845, 'chr9_KI270720v1_random': 39050, 'chr11_KI270721v1_random': 100316, 'chr14_GL000009v2_random': 201709, 'chr14_GL000225v1_random': 211173, 'chr14_KI270722v1_random': 194050, 'chr14_GL000194v1_random': 191469, 'chr14_KI270723v1_random': 38115, 'chr14_KI270724v1_random': 39555, 'chr14_KI270725v1_random': 172810, 'chr14_KI270726v1_random': 43739, 'chr15_KI270727v1_random': 448248, 'chr16_KI270728v1_random': 1872759, 'chr17_GL000205v2_random': 185591, 'chr17_KI270729v1_random': 280839, 'chr17_KI270730v1_random': 112551, 'chr22_KI270731v1_random': 150754, 'chr22_KI270732v1_random': 41543, 'chr22_KI270733v1_random': 179772, 'chr22_KI270734v1_random': 165050, 'chr22_KI270735v1_random': 42811, 'chr22_KI270736v1_random': 181920, 'chr22_KI270737v1_random': 103838, 'chr22_KI270738v1_random': 99375, 'chr22_KI270739v1_random': 73985, 'chrY_KI270740v1_random': 37240, 'chrUn_KI270302v1': 2274, 'chrUn_KI270304v1': 2165, 'chrUn_KI270303v1': 1942, 'chrUn_KI270305v1': 1472, 'chrUn_KI270322v1': 21476, 'chrUn_KI270320v1': 4416, 'chrUn_KI270310v1': 1201, 'chrUn_KI270316v1': 1444, 'chrUn_KI270315v1': 2276, 'chrUn_KI270312v1': 998, 'chrUn_KI270311v1': 12399, 'chrUn_KI270317v1': 37690, 'chrUn_KI270412v1': 1179, 'chrUn_KI270411v1': 2646, 'chrUn_KI270414v1': 2489, 'chrUn_KI270419v1': 1029, 'chrUn_KI270418v1': 2145, 'chrUn_KI270420v1': 2321, 'chrUn_KI270424v1': 2140, 'chrUn_KI270417v1': 2043, 'chrUn_KI270422v1': 1445, 'chrUn_KI270423v1': 981, 'chrUn_KI270425v1': 1884, 'chrUn_KI270429v1': 1361, 'chrUn_KI270442v1': 392061, 'chrUn_KI270466v1': 1233, 'chrUn_KI270465v1': 1774, 'chrUn_KI270467v1': 3920, 'chrUn_KI270435v1': 92983, 'chrUn_KI270438v1': 112505, 'chrUn_KI270468v1': 4055, 'chrUn_KI270510v1': 2415, 'chrUn_KI270509v1': 2318, 'chrUn_KI270518v1': 2186, 'chrUn_KI270508v1': 1951, 'chrUn_KI270516v1': 1300, 'chrUn_KI270512v1': 22689, 'chrUn_KI270519v1': 138126, 'chrUn_KI270522v1': 5674, 'chrUn_KI270511v1': 8127, 'chrUn_KI270515v1': 6361, 'chrUn_KI270507v1': 5353, 'chrUn_KI270517v1': 3253, 'chrUn_KI270529v1': 1899, 'chrUn_KI270528v1': 2983, 'chrUn_KI270530v1': 2168, 'chrUn_KI270539v1': 993, 'chrUn_KI270538v1': 91309, 'chrUn_KI270544v1': 1202, 'chrUn_KI270548v1': 1599, 'chrUn_KI270583v1': 1400, 'chrUn_KI270587v1': 2969, 'chrUn_KI270580v1': 1553, 'chrUn_KI270581v1': 7046, 'chrUn_KI270579v1': 31033, 'chrUn_KI270589v1': 44474, 'chrUn_KI270590v1': 4685, 'chrUn_KI270584v1': 4513, 'chrUn_KI270582v1': 6504, 'chrUn_KI270588v1': 6158, 'chrUn_KI270593v1': 3041, 'chrUn_KI270591v1': 5796, 'chrUn_KI270330v1': 1652, 'chrUn_KI270329v1': 1040, 'chrUn_KI270334v1': 1368, 'chrUn_KI270333v1': 2699, 'chrUn_KI270335v1': 1048, 'chrUn_KI270338v1': 1428, 'chrUn_KI270340v1': 1428, 'chrUn_KI270336v1': 1026, 'chrUn_KI270337v1': 1121, 'chrUn_KI270363v1': 1803, 'chrUn_KI270364v1': 2855, 'chrUn_KI270362v1': 3530, 'chrUn_KI270366v1': 8320, 'chrUn_KI270378v1': 1048, 'chrUn_KI270379v1': 1045, 'chrUn_KI270389v1': 1298, 'chrUn_KI270390v1': 2387, 'chrUn_KI270387v1': 1537, 'chrUn_KI270395v1': 1143, 'chrUn_KI270396v1': 1880, 'chrUn_KI270388v1': 1216, 'chrUn_KI270394v1': 970, 'chrUn_KI270386v1': 1788, 'chrUn_KI270391v1': 1484, 'chrUn_KI270383v1': 1750, 'chrUn_KI270393v1': 1308, 'chrUn_KI270384v1': 1658, 'chrUn_KI270392v1': 971, 'chrUn_KI270381v1': 1930, 'chrUn_KI270385v1': 990, 'chrUn_KI270382v1': 4215, 'chrUn_KI270376v1': 1136, 'chrUn_KI270374v1': 2656, 'chrUn_KI270372v1': 1650, 'chrUn_KI270373v1': 1451, 'chrUn_KI270375v1': 2378, 'chrUn_KI270371v1': 2805, 'chrUn_KI270448v1': 7992, 'chrUn_KI270521v1': 7642, 'chrUn_GL000195v1': 182896, 'chrUn_GL000219v1': 179198, 'chrUn_GL000220v1': 161802, 'chrUn_GL000224v1': 179693, 'chrUn_KI270741v1': 157432, 'chrUn_GL000226v1': 15008, 'chrUn_GL000213v1': 164239, 'chrUn_KI270743v1': 210658, 'chrUn_KI270744v1': 168472, 'chrUn_KI270745v1': 41891, 'chrUn_KI270746v1': 66486, 'chrUn_KI270747v1': 198735, 'chrUn_KI270748v1': 93321, 'chrUn_KI270749v1': 158759, 'chrUn_KI270750v1': 148850, 'chrUn_KI270751v1': 150742, 'chrUn_KI270752v1': 27745, 'chrUn_KI270753v1': 62944, 'chrUn_KI270754v1': 40191, 'chrUn_KI270755v1': 36723, 'chrUn_KI270756v1': 79590, 'chrUn_KI270757v1': 71251, 'chrUn_GL000214v1': 137718, 'chrUn_KI270742v1': 186739, 'chrUn_GL000216v2': 176608, 'chrUn_GL000218v1': 161147, 'chrEBV': 171823}\n", - "\tContig chr17\n", - "16 total jobs\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 26A20G52\n", - "CIGAR tag 1S100M\n", - "is_reverse False\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse True\n", - "read id VH01429:22:AACFJ5NHV:1:2211:40480:18323\n", - "VH01429:22:AACFJ5NHV:1:2211:40480:18323\t99\t#16\t43044305\t255\t1S100M\t#16\t43044312\t107\tGTGCTACCAAGTTTATTTGCAGTGTTACCAGCACAACATTTACAAAACATATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGA\tarray('B', [12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 26, 12, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 26, 34, 34, 34, 34])\t[('MD', '26A20G52'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 2), ('AS', 190)]\n", - "reverse_or_forward: -\n", - "----------------------------\n", - "MD tag: 26A20G52\n", - "CIGAR string 1S100M\n", - "Reference seq: TGCTACCAAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACGTATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGA\n", - "Aligned seq: GTGCTACCAAGTTTATTTGCAGTGTTACCAGCACAACATTTACAAAACATATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGA\n", - "Qualities: array('B', [12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 26, 12, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 26, 34, 34, 34, 34])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 1), (0, 100)]\n", - "Aligned sequence before clipping (if needed):\n", - " GTGCTACCAAGTTTATTTGCAGTGTTACCAGCACAACATTTACAAAACATATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGA\n", - "Qualities before clipping:\n", - " array('B', [12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 26, 12, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 26, 34, 34, 34, 34])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 100)]\n", - "Aligned sequence after clipping (if needed):\n", - " TGCTACCAAGTTTATTTGCAGTGTTACCAGCACAACATTTACAAAACATATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGA\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 26, 12, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 26, 34, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['26', '20', '52']\n", - "[26, 47, 100]\n", - "Indicated reference seq:\n", - " tgctaccaagtttatttgcagtgttaAcagcacaacatttacaaaacGtattttgtacaatcaagtcttcactgcccttgcacactgggggggctaggga\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " tgctaccaagtttatttgcagtgttaAcagcacaacatttacaaaacGtattttgtacaatcaagtcttcactgcccttgcacactgggggggctaggga\n", - "Fixed aligned seq:\n", - " TGCTACCAAGTTTATTTGCAGTGTTACCAGCACAACATTTACAAAACATATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGA\n", - "Finalized fixed aligned seq:\n", - " tgctaccaagtttatttgcagtgttaCcagcacaacatttacaaaacAtattttgtacaatcaagtcttcactgcccttgcacactgggggggctaggga\n", - "Indicated qualities:\n", - " 34343434343434343434263434343434343434342634343434261234343434342626343434343434343434341234341234343434343434123434343434343412343434343412343434343434343434342634342634343426343426343434342634343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['C', 'A']\n", - "ref bases ['A', 'G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['C', 'A'], ref bases: ['A', 'G']\n", - "Getting info: C A 12 27\n", - "Getting info: A G 12 48\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 40G3T55\n", - "CIGAR tag 100M1S\n", - "is_reverse True\n", - "is_read1 False\n", - "is_read2 True\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id VH01429:22:AACFJ5NHV:1:2211:40480:18323\n", - "VH01429:22:AACFJ5NHV:1:2211:40480:18323\t147\t#16\t43044312\t255\t100M1S\t#16\t43044305\t-107\tAAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACATATGTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGAAGACCTAC\tarray('B', [34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 12])\t[('MD', '40G3T55'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 2), ('AS', 190)]\n", - "reverse_or_forward: -\n", - "----------------------------\n", - "MD tag: 40G3T55\n", - "CIGAR string 100M1S\n", - "Reference seq: AAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACGTATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGAAGACCTA\n", - "Aligned seq: AAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACATATGTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGAAGACCTAC\n", - "Qualities: array('B', [34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 12])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(0, 100), (4, 1)]\n", - "Aligned sequence before clipping (if needed):\n", - " AAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACATATGTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGAAGACCTAC\n", - "Qualities before clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 12])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 100)]\n", - "Aligned sequence after clipping (if needed):\n", - " AAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACATATGTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGAAGACCTA\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['40', '3', '55']\n", - "[40, 44, 100]\n", - "Indicated reference seq:\n", - " aagtttatttgcagtgttaacagcacaacatttacaaaacGtatTttgtacaatcaagtcttcactgcccttgcacactgggggggctagggaagaccta\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " aagtttatttgcagtgttaacagcacaacatttacaaaacGtatTttgtacaatcaagtcttcactgcccttgcacactgggggggctagggaagaccta\n", - "Fixed aligned seq:\n", - " AAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACATATGTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGAAGACCTA\n", - "Finalized fixed aligned seq:\n", - " aagtttatttgcagtgttaacagcacaacatttacaaaacAtatGttgtacaatcaagtcttcactgcccttgcacactgggggggctagggaagaccta\n", - "Indicated qualities:\n", - " 34343434343434263434342634343434341234343434263434343434343434343434343426343434343434341234343434343434343434343434263412343434343434343434342634343434343434343434343434343426343434263434343434343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['A', 'G']\n", - "ref bases ['G', 'T']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['A', 'G'], ref bases: ['G', 'T']\n", - "chr17:002, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:006, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:007, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:004, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:005, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:003, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:012, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:010, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:009, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:011, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:013, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:000, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:014, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:001, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:015, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "Getting info: A G 34 41\n", - "Getting info: G T 12 45\n", - "chr17:008, total reads: 2, counts_df: chr17\n", - "edited 2\n", - "Reads processed:\t2\n", - "Time to process reads in min:\t0.02926\n", - "Summary:\t chr17\n", - "edited 2\n", - "\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Calculating coverage at edited sites, minimum read quality is 0...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "\tsplit chr17_000_0_5203591, 0/16...\n", - "\tsplit chr17_010_52035910_57239501, 10/16...\n", - "Done grouping! Concatenating ...\n", - "Done concatenating!\n", - "edit_info_grouped_per_contig_combined dict_keys(['chr17_000_0_5203591', 'chr17_001_5203591_10407182', 'chr17_002_10407182_15610773', 'chr17_003_15610773_20814364', 'chr17_004_20814364_26017955', 'chr17_005_26017955_31221546', 'chr17_006_31221546_36425137', 'chr17_007_36425137_41628728', 'chr17_008_41628728_46832319', 'chr17_009_46832319_52035910', 'chr17_010_52035910_57239501', 'chr17_011_57239501_62443092', 'chr17_012_62443092_67646683', 'chr17_013_67646683_72850274', 'chr17_014_72850274_78053865', 'chr17_015_78053865_83257456'])\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "100%|██████████| 16/16 [00:01<00:00, 9.80it/s]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "~~~~~~\n", - "!!!!SINGLE END!!!!!\n", - "~~~~~~~`\n", - "~~~~~~\n", - "!!!!SINGLE END!!!!!\n", - "~~~~~~~`\n", - "~~~~~~\n", - "!!!!SINGLE END!!!!!\n", - "~~~~~~~`\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "100%|██████████| 16/16 [00:01<00:00, 11.70it/s]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Concatenating results...\n", - "Done concatenating.\n", - "Total time to calculate coverage: 0.024 minutes\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Filtering and calculating site-level statistics\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Loading edit information...\n", - "Filtering..\n", - "~~~~~~~~~~~~~~~~~~~~~~~\n", - "Filtering edited sites\n", - "~~~~~~~~~~~~~~~~~~~~~~~\n", - "Minimum distance from end = 0, Minimum base-calling quality = 0\n", - "Deduplicating....\n", - "\tNumber of edits before filtering:\n", - "\t4\n", - "\tNumber of edits after filtering:\n", - "\t4\n", - "\tNumber of edits after deduplicating:\n", - "\t3\n", - "\tNumber of unique edit sites:\n", - "\t3\n", - "Writing sites...\n", - "\n", - "Adding strand-specific conversion...\n", + "Making bedgraphs for ['CT'] conversions...\n", "\n", - "3 sites being converted to SAILOR format...\n", - "0 rows had coverage of 0 or more edits than coverage... filtering these out, but look into them...\n", - "1 final deduplicated SAILOR-formatted sites\n", "Annotating sites with GTF information from /tscc/projects/ps-yeolab3/ekofman/sailor2//annotations/hg38_gencode.v35.annotation.genes.bed...\n", - "Current memory usage 21.384422MB; Peak: 22.496814MB\n", - "Time elapsed: 4.34s\n", - "++++++\n", - "Done!\n", - "++++++\n", - "F1R2_pair_test\n", - "Removing old files...\n", - "Running tests...\n", - "Assuming 16 cores available for multiprocessing. Set this to the number of available cores for optimal execution.\n", - "Arguments:\n", - "\tBAM filepath:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/bams/F1R2_pair.bam\n", - "\tAnnotation bedfile filepath:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//annotations/hg38_gencode.v35.annotation.genes.bed\n", - "\tOutput folder:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/F1R2_pair_test\n", - "\tBarcode whitelist:\tNone\n", - "\tStrandedness:\t2\n", - "\tBarcode Tag:\tNone\n", - "\tPaired End:\tTrue\n", - "\tCoverage only:\tFalse\n", - "\tFiltering only:\tFalse\n", - "\tAnnotation only:\tFalse\n", - "\tSailor outputs:\tTrue\n", - "\tMinimum base quality:\t0\n", - "\tMinimum read quality:\t0\n", - "\tMinimum distance from end:\t0\n", - "\tmax_edits_per_read:\tNone\n", - "\tContigs:\tchr17\n", - "\tNumber of intervals:\t16\n", - "\tCores:\t16\n", - "\tVerbose:\tTrue\n", - "\tSkip coverage?:\tFalse\n", - "\n", - ":::: :::: ::: ::::::::: ::::::::::: :::: ::: :::::::::: \n", - "+:+:+: :+:+:+ :+: :+: :+: :+: :+: :+:+: :+: :+: \n", - "+:+ +:+:+ +:+ +:+ +:+ +:+ +:+ +:+ :+:+:+ +:+ +:+ \n", - "+#+ +:+ +#+ +#++:++#++: +#++:++#: +#+ +#+ +:+ +#+ +#++:++# \n", - "+#+ +#+ +#+ +#+ +#+ +#+ +#+ +#+ +#+#+# +#+ \n", - "#+# #+# #+# #+# #+# #+# #+# #+# #+#+# #+# \n", - "### ### ### ### ### ### ########### ### #### ########## \n", - "==================================================================\n", - "Multi-core Algorithm for Rapid Identification of Nucleotide Edits\n", - "==================================================================\n", - "~~~~~~~~~~~~~~~~~~\n", - "Identifying edits\n", - "~~~~~~~~~~~~~~~~~~\n", - "Each contig is being split into 16 subsets...\n", - "contig_lengths_dict:{'chr1': 248956422, 'chr2': 242193529, 'chr3': 198295559, 'chr4': 190214555, 'chr5': 181538259, 'chr6': 170805979, 'chr7': 159345973, 'chr8': 145138636, 'chr9': 138394717, 'chr10': 133797422, 'chr11': 135086622, 'chr12': 133275309, 'chr13': 114364328, 'chr14': 107043718, 'chr15': 101991189, 'chr16': 90338345, 'chr17': 83257441, 'chr18': 80373285, 'chr19': 58617616, 'chr20': 64444167, 'chr21': 46709983, 'chr22': 50818468, 'chrX': 156040895, 'chrY': 57227415, 'chrM': 16569, 'chr1_KI270706v1_random': 175055, 'chr1_KI270707v1_random': 32032, 'chr1_KI270708v1_random': 127682, 'chr1_KI270709v1_random': 66860, 'chr1_KI270710v1_random': 40176, 'chr1_KI270711v1_random': 42210, 'chr1_KI270712v1_random': 176043, 'chr1_KI270713v1_random': 40745, 'chr1_KI270714v1_random': 41717, 'chr2_KI270715v1_random': 161471, 'chr2_KI270716v1_random': 153799, 'chr3_GL000221v1_random': 155397, 'chr4_GL000008v2_random': 209709, 'chr5_GL000208v1_random': 92689, 'chr9_KI270717v1_random': 40062, 'chr9_KI270718v1_random': 38054, 'chr9_KI270719v1_random': 176845, 'chr9_KI270720v1_random': 39050, 'chr11_KI270721v1_random': 100316, 'chr14_GL000009v2_random': 201709, 'chr14_GL000225v1_random': 211173, 'chr14_KI270722v1_random': 194050, 'chr14_GL000194v1_random': 191469, 'chr14_KI270723v1_random': 38115, 'chr14_KI270724v1_random': 39555, 'chr14_KI270725v1_random': 172810, 'chr14_KI270726v1_random': 43739, 'chr15_KI270727v1_random': 448248, 'chr16_KI270728v1_random': 1872759, 'chr17_GL000205v2_random': 185591, 'chr17_KI270729v1_random': 280839, 'chr17_KI270730v1_random': 112551, 'chr22_KI270731v1_random': 150754, 'chr22_KI270732v1_random': 41543, 'chr22_KI270733v1_random': 179772, 'chr22_KI270734v1_random': 165050, 'chr22_KI270735v1_random': 42811, 'chr22_KI270736v1_random': 181920, 'chr22_KI270737v1_random': 103838, 'chr22_KI270738v1_random': 99375, 'chr22_KI270739v1_random': 73985, 'chrY_KI270740v1_random': 37240, 'chrUn_KI270302v1': 2274, 'chrUn_KI270304v1': 2165, 'chrUn_KI270303v1': 1942, 'chrUn_KI270305v1': 1472, 'chrUn_KI270322v1': 21476, 'chrUn_KI270320v1': 4416, 'chrUn_KI270310v1': 1201, 'chrUn_KI270316v1': 1444, 'chrUn_KI270315v1': 2276, 'chrUn_KI270312v1': 998, 'chrUn_KI270311v1': 12399, 'chrUn_KI270317v1': 37690, 'chrUn_KI270412v1': 1179, 'chrUn_KI270411v1': 2646, 'chrUn_KI270414v1': 2489, 'chrUn_KI270419v1': 1029, 'chrUn_KI270418v1': 2145, 'chrUn_KI270420v1': 2321, 'chrUn_KI270424v1': 2140, 'chrUn_KI270417v1': 2043, 'chrUn_KI270422v1': 1445, 'chrUn_KI270423v1': 981, 'chrUn_KI270425v1': 1884, 'chrUn_KI270429v1': 1361, 'chrUn_KI270442v1': 392061, 'chrUn_KI270466v1': 1233, 'chrUn_KI270465v1': 1774, 'chrUn_KI270467v1': 3920, 'chrUn_KI270435v1': 92983, 'chrUn_KI270438v1': 112505, 'chrUn_KI270468v1': 4055, 'chrUn_KI270510v1': 2415, 'chrUn_KI270509v1': 2318, 'chrUn_KI270518v1': 2186, 'chrUn_KI270508v1': 1951, 'chrUn_KI270516v1': 1300, 'chrUn_KI270512v1': 22689, 'chrUn_KI270519v1': 138126, 'chrUn_KI270522v1': 5674, 'chrUn_KI270511v1': 8127, 'chrUn_KI270515v1': 6361, 'chrUn_KI270507v1': 5353, 'chrUn_KI270517v1': 3253, 'chrUn_KI270529v1': 1899, 'chrUn_KI270528v1': 2983, 'chrUn_KI270530v1': 2168, 'chrUn_KI270539v1': 993, 'chrUn_KI270538v1': 91309, 'chrUn_KI270544v1': 1202, 'chrUn_KI270548v1': 1599, 'chrUn_KI270583v1': 1400, 'chrUn_KI270587v1': 2969, 'chrUn_KI270580v1': 1553, 'chrUn_KI270581v1': 7046, 'chrUn_KI270579v1': 31033, 'chrUn_KI270589v1': 44474, 'chrUn_KI270590v1': 4685, 'chrUn_KI270584v1': 4513, 'chrUn_KI270582v1': 6504, 'chrUn_KI270588v1': 6158, 'chrUn_KI270593v1': 3041, 'chrUn_KI270591v1': 5796, 'chrUn_KI270330v1': 1652, 'chrUn_KI270329v1': 1040, 'chrUn_KI270334v1': 1368, 'chrUn_KI270333v1': 2699, 'chrUn_KI270335v1': 1048, 'chrUn_KI270338v1': 1428, 'chrUn_KI270340v1': 1428, 'chrUn_KI270336v1': 1026, 'chrUn_KI270337v1': 1121, 'chrUn_KI270363v1': 1803, 'chrUn_KI270364v1': 2855, 'chrUn_KI270362v1': 3530, 'chrUn_KI270366v1': 8320, 'chrUn_KI270378v1': 1048, 'chrUn_KI270379v1': 1045, 'chrUn_KI270389v1': 1298, 'chrUn_KI270390v1': 2387, 'chrUn_KI270387v1': 1537, 'chrUn_KI270395v1': 1143, 'chrUn_KI270396v1': 1880, 'chrUn_KI270388v1': 1216, 'chrUn_KI270394v1': 970, 'chrUn_KI270386v1': 1788, 'chrUn_KI270391v1': 1484, 'chrUn_KI270383v1': 1750, 'chrUn_KI270393v1': 1308, 'chrUn_KI270384v1': 1658, 'chrUn_KI270392v1': 971, 'chrUn_KI270381v1': 1930, 'chrUn_KI270385v1': 990, 'chrUn_KI270382v1': 4215, 'chrUn_KI270376v1': 1136, 'chrUn_KI270374v1': 2656, 'chrUn_KI270372v1': 1650, 'chrUn_KI270373v1': 1451, 'chrUn_KI270375v1': 2378, 'chrUn_KI270371v1': 2805, 'chrUn_KI270448v1': 7992, 'chrUn_KI270521v1': 7642, 'chrUn_GL000195v1': 182896, 'chrUn_GL000219v1': 179198, 'chrUn_GL000220v1': 161802, 'chrUn_GL000224v1': 179693, 'chrUn_KI270741v1': 157432, 'chrUn_GL000226v1': 15008, 'chrUn_GL000213v1': 164239, 'chrUn_KI270743v1': 210658, 'chrUn_KI270744v1': 168472, 'chrUn_KI270745v1': 41891, 'chrUn_KI270746v1': 66486, 'chrUn_KI270747v1': 198735, 'chrUn_KI270748v1': 93321, 'chrUn_KI270749v1': 158759, 'chrUn_KI270750v1': 148850, 'chrUn_KI270751v1': 150742, 'chrUn_KI270752v1': 27745, 'chrUn_KI270753v1': 62944, 'chrUn_KI270754v1': 40191, 'chrUn_KI270755v1': 36723, 'chrUn_KI270756v1': 79590, 'chrUn_KI270757v1': 71251, 'chrUn_GL000214v1': 137718, 'chrUn_KI270742v1': 186739, 'chrUn_GL000216v2': 176608, 'chrUn_GL000218v1': 161147, 'chrEBV': 171823}\n", - "\tContig chr17\n", - "16 total jobs\n", - "chr17:000, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:003, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 26A20G52\n", - "CIGAR tag 1S100M\n", - "is_reverse False\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse True\n", - "read id VH01429:22:AACFJ5NHV:1:2211:40480:18323\n", - "VH01429:22:AACFJ5NHV:1:2211:40480:18323\t99\t#16\t43044305\t255\t1S100M\t#16\t43044312\t107\tGTGCTACCAAGTTTATTTGCAGTGTTACCAGCACAACATTTACAAAACATATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGA\tarray('B', [12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 26, 12, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 26, 34, 34, 34, 34])\t[('MD', '26A20G52'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 2), ('AS', 190)]\n", - "reverse_or_forward: -\n", - "----------------------------\n", - "MD tag: 26A20G52\n", - "CIGAR string 1S100M\n", - "Reference seq: TGCTACCAAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACGTATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGA\n", - "Aligned seq: GTGCTACCAAGTTTATTTGCAGTGTTACCAGCACAACATTTACAAAACATATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGA\n", - "Qualities: array('B', [12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 26, 12, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 26, 34, 34, 34, 34])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 1), (0, 100)]\n", - "Aligned sequence before clipping (if needed):\n", - " GTGCTACCAAGTTTATTTGCAGTGTTACCAGCACAACATTTACAAAACATATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGA\n", - "Qualities before clipping:\n", - " array('B', [12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 26, 12, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 26, 34, 34, 34, 34])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 100)]\n", - "Aligned sequence after clipping (if needed):\n", - " TGCTACCAAGTTTATTTGCAGTGTTACCAGCACAACATTTACAAAACATATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGA\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 26, 12, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 26, 34, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['26', '20', '52']\n", - "[26, 47, 100]\n", - "Indicated reference seq:\n", - " tgctaccaagtttatttgcagtgttaAcagcacaacatttacaaaacGtattttgtacaatcaagtcttcactgcccttgcacactgggggggctaggga\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " tgctaccaagtttatttgcagtgttaAcagcacaacatttacaaaacGtattttgtacaatcaagtcttcactgcccttgcacactgggggggctaggga\n", - "Fixed aligned seq:\n", - " TGCTACCAAGTTTATTTGCAGTGTTACCAGCACAACATTTACAAAACATATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGA\n", - "Finalized fixed aligned seq:\n", - " tgctaccaagtttatttgcagtgttaCcagcacaacatttacaaaacAtattttgtacaatcaagtcttcactgcccttgcacactgggggggctaggga\n", - "Indicated qualities:\n", - " 34343434343434343434263434343434343434342634343434261234343434342626343434343434343434341234341234343434343434123434343434343412343434343412343434343434343434342634342634343426343426343434342634343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['C', 'A']\n", - "ref bases ['A', 'G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['C', 'A'], ref bases: ['A', 'G']\n", - "Getting info: C A 12 27\n", - "Getting info: A G 12 48\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 40G3T55\n", - "CIGAR tag 100M1S\n", - "is_reverse True\n", - "is_read1 False\n", - "is_read2 True\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id VH01429:22:AACFJ5NHV:1:2211:40480:18323\n", - "VH01429:22:AACFJ5NHV:1:2211:40480:18323\t147\t#16\t43044312\t255\t100M1S\t#16\t43044305\t-107\tAAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACATATGTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGAAGACCTAC\tarray('B', [34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 12])\t[('MD', '40G3T55'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 2), ('AS', 190)]\n", - "reverse_or_forward: -\n", - "----------------------------\n", - "MD tag: 40G3T55\n", - "CIGAR string 100M1S\n", - "Reference seq: AAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACGTATTTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGAAGACCTA\n", - "Aligned seq: AAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACATATGTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGAAGACCTAC\n", - "Qualities: array('B', [34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 12])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(0, 100), (4, 1)]\n", - "Aligned sequence before clipping (if needed):\n", - " AAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACATATGTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGAAGACCTAC\n", - "Qualities before clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 12])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 100)]\n", - "Aligned sequence after clipping (if needed):\n", - " AAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACATATGTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGAAGACCTA\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['40', '3', '55']\n", - "[40, 44, 100]\n", - "Indicated reference seq:\n", - " aagtttatttgcagtgttaacagcacaacatttacaaaacGtatTttgtacaatcaagtcttcactgcccttgcacactgggggggctagggaagaccta\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " aagtttatttgcagtgttaacagcacaacatttacaaaacGtatTttgtacaatcaagtcttcactgcccttgcacactgggggggctagggaagaccta\n", - "Fixed aligned seq:\n", - " AAGTTTATTTGCAGTGTTAACAGCACAACATTTACAAAACATATGTTGTACAATCAAGTCTTCACTGCCCTTGCACACTGGGGGGGCTAGGGAAGACCTA\n", - "Finalized fixed aligned seq:\n", - " aagtttatttgcagtgttaacagcacaacatttacaaaacAtatGttgtacaatcaagtcttcactgcccttgcacactgggggggctagggaagaccta\n", - "Indicated qualities:\n", - " 34343434343434263434342634343434341234343434263434343434343434343434343426343434343434341234343434343434343434343434263412343434343434343434342634343434343434343434343434343426343434263434343434343434\n", - "chr17:001, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:002, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:004, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:010, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:005, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:009, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:011, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:012, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:014, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:007, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:015, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:006, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:013, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['A', 'G']\n", - "ref bases ['G', 'T']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['A', 'G'], ref bases: ['G', 'T']\n", - "Getting info: A G 34 41\n", - "Getting info: G T 12 45\n", - "chr17:008, total reads: 2, counts_df: chr17\n", - "edited 2\n", - "Reads processed:\t2\n", - "Time to process reads in min:\t0.02389\n", - "Summary:\t chr17\n", - "edited 2\n", - "\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Calculating coverage at edited sites, minimum read quality is 0...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "\tsplit chr17_000_0_5203591, 0/16...\n", - "\tsplit chr17_010_52035910_57239501, 10/16...\n", - "Done grouping! Concatenating ...\n", - "Done concatenating!\n", - "edit_info_grouped_per_contig_combined dict_keys(['chr17_000_0_5203591', 'chr17_001_5203591_10407182', 'chr17_002_10407182_15610773', 'chr17_003_15610773_20814364', 'chr17_004_20814364_26017955', 'chr17_005_26017955_31221546', 'chr17_006_31221546_36425137', 'chr17_007_36425137_41628728', 'chr17_008_41628728_46832319', 'chr17_009_46832319_52035910', 'chr17_010_52035910_57239501', 'chr17_011_57239501_62443092', 'chr17_012_62443092_67646683', 'chr17_013_67646683_72850274', 'chr17_014_72850274_78053865', 'chr17_015_78053865_83257456'])\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "100%|██████████| 16/16 [00:01<00:00, 12.10it/s]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/F1R2_pair_test/split_bams/chr17/chr17_008_41628728_46832319.bam.sorted.bam\n", - " chr17:43044352~~~~~~~`\n", - "coverage_at_pos 1\n", - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/F1R2_pair_test/split_bams/chr17/chr17_008_41628728_46832319.bam.sorted.bam\n", - " chr17:43044331~~~~~~~`\n", - "coverage_at_pos 1\n", - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/F1R2_pair_test/split_bams/chr17/chr17_008_41628728_46832319.bam.sorted.bam\n", - " chr17:43044356~~~~~~~`\n", - "coverage_at_pos 1\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "100%|██████████| 16/16 [00:01<00:00, 12.33it/s]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Concatenating results...\n", - "Done concatenating.\n", - "Total time to calculate coverage: 0.023 minutes\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Filtering and calculating site-level statistics\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Loading edit information...\n", - "Filtering..\n", - "~~~~~~~~~~~~~~~~~~~~~~~\n", - "Filtering edited sites\n", - "~~~~~~~~~~~~~~~~~~~~~~~\n", - "Minimum distance from end = 0, Minimum base-calling quality = 0\n", - "Deduplicating....\n", - "\tNumber of edits before filtering:\n", - "\t4\n", - "\tNumber of edits after filtering:\n", - "\t4\n", - "\tNumber of edits after deduplicating:\n", - "\t3\n", - "\tNumber of unique edit sites:\n", - "\t3\n", - "Writing sites...\n", - "\n", - "Adding strand-specific conversion...\n", - "\n", - "3 sites being converted to SAILOR format...\n", - "0 rows had coverage of 0 or more edits than coverage... filtering these out, but look into them...\n", - "1 final deduplicated SAILOR-formatted sites\n", - "Annotating sites with GTF information from /tscc/projects/ps-yeolab3/ekofman/sailor2//annotations/hg38_gencode.v35.annotation.genes.bed...\n", - "Current memory usage 21.381979MB; Peak: 22.494346MB\n", - "Time elapsed: 3.76s\n", - "++++++\n", - "Done!\n", - "++++++\n", - "F2R1_end_second_in_pair_test\n", - "Removing old files...\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "rm: cannot remove 'tests/strandedness_tests/F2R1_end_second_in_pair_test/*': No such file or directory\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Running tests...\n", - "Assuming 16 cores available for multiprocessing. Set this to the number of available cores for optimal execution.\n", - "Arguments:\n", - "\tBAM filepath:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/bams/F2R1_end_second_in_pair.bam\n", - "\tAnnotation bedfile filepath:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//annotations/hg38_gencode.v35.annotation.genes.bed\n", - "\tOutput folder:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/F2R1_end_second_in_pair_test\n", - "\tBarcode whitelist:\tNone\n", - "\tStrandedness:\t2\n", - "\tBarcode Tag:\tNone\n", - "\tPaired End:\tTrue\n", - "\tCoverage only:\tFalse\n", - "\tFiltering only:\tFalse\n", - "\tAnnotation only:\tFalse\n", - "\tSailor outputs:\tTrue\n", - "\tMinimum base quality:\t0\n", - "\tMinimum read quality:\t0\n", - "\tMinimum distance from end:\t0\n", - "\tmax_edits_per_read:\tNone\n", - "\tContigs:\tchr17\n", - "\tNumber of intervals:\t16\n", - "\tCores:\t16\n", - "\tVerbose:\tTrue\n", - "\tSkip coverage?:\tFalse\n", - "\n", - ":::: :::: ::: ::::::::: ::::::::::: :::: ::: :::::::::: \n", - "+:+:+: :+:+:+ :+: :+: :+: :+: :+: :+:+: :+: :+: \n", - "+:+ +:+:+ +:+ +:+ +:+ +:+ +:+ +:+ :+:+:+ +:+ +:+ \n", - "+#+ +:+ +#+ +#++:++#++: +#++:++#: +#+ +#+ +:+ +#+ +#++:++# \n", - "+#+ +#+ +#+ +#+ +#+ +#+ +#+ +#+ +#+#+# +#+ \n", - "#+# #+# #+# #+# #+# #+# #+# #+# #+#+# #+# \n", - "### ### ### ### ### ### ########### ### #### ########## \n", - "==================================================================\n", - "Multi-core Algorithm for Rapid Identification of Nucleotide Edits\n", - "==================================================================\n", - "~~~~~~~~~~~~~~~~~~\n", - "Identifying edits\n", - "~~~~~~~~~~~~~~~~~~\n", - "Each contig is being split into 16 subsets...\n", - "contig_lengths_dict:{'chr1': 248956422, 'chr2': 242193529, 'chr3': 198295559, 'chr4': 190214555, 'chr5': 181538259, 'chr6': 170805979, 'chr7': 159345973, 'chr8': 145138636, 'chr9': 138394717, 'chr10': 133797422, 'chr11': 135086622, 'chr12': 133275309, 'chr13': 114364328, 'chr14': 107043718, 'chr15': 101991189, 'chr16': 90338345, 'chr17': 83257441, 'chr18': 80373285, 'chr19': 58617616, 'chr20': 64444167, 'chr21': 46709983, 'chr22': 50818468, 'chrX': 156040895, 'chrY': 57227415, 'chrM': 16569, 'chr1_KI270706v1_random': 175055, 'chr1_KI270707v1_random': 32032, 'chr1_KI270708v1_random': 127682, 'chr1_KI270709v1_random': 66860, 'chr1_KI270710v1_random': 40176, 'chr1_KI270711v1_random': 42210, 'chr1_KI270712v1_random': 176043, 'chr1_KI270713v1_random': 40745, 'chr1_KI270714v1_random': 41717, 'chr2_KI270715v1_random': 161471, 'chr2_KI270716v1_random': 153799, 'chr3_GL000221v1_random': 155397, 'chr4_GL000008v2_random': 209709, 'chr5_GL000208v1_random': 92689, 'chr9_KI270717v1_random': 40062, 'chr9_KI270718v1_random': 38054, 'chr9_KI270719v1_random': 176845, 'chr9_KI270720v1_random': 39050, 'chr11_KI270721v1_random': 100316, 'chr14_GL000009v2_random': 201709, 'chr14_GL000225v1_random': 211173, 'chr14_KI270722v1_random': 194050, 'chr14_GL000194v1_random': 191469, 'chr14_KI270723v1_random': 38115, 'chr14_KI270724v1_random': 39555, 'chr14_KI270725v1_random': 172810, 'chr14_KI270726v1_random': 43739, 'chr15_KI270727v1_random': 448248, 'chr16_KI270728v1_random': 1872759, 'chr17_GL000205v2_random': 185591, 'chr17_KI270729v1_random': 280839, 'chr17_KI270730v1_random': 112551, 'chr22_KI270731v1_random': 150754, 'chr22_KI270732v1_random': 41543, 'chr22_KI270733v1_random': 179772, 'chr22_KI270734v1_random': 165050, 'chr22_KI270735v1_random': 42811, 'chr22_KI270736v1_random': 181920, 'chr22_KI270737v1_random': 103838, 'chr22_KI270738v1_random': 99375, 'chr22_KI270739v1_random': 73985, 'chrY_KI270740v1_random': 37240, 'chrUn_KI270302v1': 2274, 'chrUn_KI270304v1': 2165, 'chrUn_KI270303v1': 1942, 'chrUn_KI270305v1': 1472, 'chrUn_KI270322v1': 21476, 'chrUn_KI270320v1': 4416, 'chrUn_KI270310v1': 1201, 'chrUn_KI270316v1': 1444, 'chrUn_KI270315v1': 2276, 'chrUn_KI270312v1': 998, 'chrUn_KI270311v1': 12399, 'chrUn_KI270317v1': 37690, 'chrUn_KI270412v1': 1179, 'chrUn_KI270411v1': 2646, 'chrUn_KI270414v1': 2489, 'chrUn_KI270419v1': 1029, 'chrUn_KI270418v1': 2145, 'chrUn_KI270420v1': 2321, 'chrUn_KI270424v1': 2140, 'chrUn_KI270417v1': 2043, 'chrUn_KI270422v1': 1445, 'chrUn_KI270423v1': 981, 'chrUn_KI270425v1': 1884, 'chrUn_KI270429v1': 1361, 'chrUn_KI270442v1': 392061, 'chrUn_KI270466v1': 1233, 'chrUn_KI270465v1': 1774, 'chrUn_KI270467v1': 3920, 'chrUn_KI270435v1': 92983, 'chrUn_KI270438v1': 112505, 'chrUn_KI270468v1': 4055, 'chrUn_KI270510v1': 2415, 'chrUn_KI270509v1': 2318, 'chrUn_KI270518v1': 2186, 'chrUn_KI270508v1': 1951, 'chrUn_KI270516v1': 1300, 'chrUn_KI270512v1': 22689, 'chrUn_KI270519v1': 138126, 'chrUn_KI270522v1': 5674, 'chrUn_KI270511v1': 8127, 'chrUn_KI270515v1': 6361, 'chrUn_KI270507v1': 5353, 'chrUn_KI270517v1': 3253, 'chrUn_KI270529v1': 1899, 'chrUn_KI270528v1': 2983, 'chrUn_KI270530v1': 2168, 'chrUn_KI270539v1': 993, 'chrUn_KI270538v1': 91309, 'chrUn_KI270544v1': 1202, 'chrUn_KI270548v1': 1599, 'chrUn_KI270583v1': 1400, 'chrUn_KI270587v1': 2969, 'chrUn_KI270580v1': 1553, 'chrUn_KI270581v1': 7046, 'chrUn_KI270579v1': 31033, 'chrUn_KI270589v1': 44474, 'chrUn_KI270590v1': 4685, 'chrUn_KI270584v1': 4513, 'chrUn_KI270582v1': 6504, 'chrUn_KI270588v1': 6158, 'chrUn_KI270593v1': 3041, 'chrUn_KI270591v1': 5796, 'chrUn_KI270330v1': 1652, 'chrUn_KI270329v1': 1040, 'chrUn_KI270334v1': 1368, 'chrUn_KI270333v1': 2699, 'chrUn_KI270335v1': 1048, 'chrUn_KI270338v1': 1428, 'chrUn_KI270340v1': 1428, 'chrUn_KI270336v1': 1026, 'chrUn_KI270337v1': 1121, 'chrUn_KI270363v1': 1803, 'chrUn_KI270364v1': 2855, 'chrUn_KI270362v1': 3530, 'chrUn_KI270366v1': 8320, 'chrUn_KI270378v1': 1048, 'chrUn_KI270379v1': 1045, 'chrUn_KI270389v1': 1298, 'chrUn_KI270390v1': 2387, 'chrUn_KI270387v1': 1537, 'chrUn_KI270395v1': 1143, 'chrUn_KI270396v1': 1880, 'chrUn_KI270388v1': 1216, 'chrUn_KI270394v1': 970, 'chrUn_KI270386v1': 1788, 'chrUn_KI270391v1': 1484, 'chrUn_KI270383v1': 1750, 'chrUn_KI270393v1': 1308, 'chrUn_KI270384v1': 1658, 'chrUn_KI270392v1': 971, 'chrUn_KI270381v1': 1930, 'chrUn_KI270385v1': 990, 'chrUn_KI270382v1': 4215, 'chrUn_KI270376v1': 1136, 'chrUn_KI270374v1': 2656, 'chrUn_KI270372v1': 1650, 'chrUn_KI270373v1': 1451, 'chrUn_KI270375v1': 2378, 'chrUn_KI270371v1': 2805, 'chrUn_KI270448v1': 7992, 'chrUn_KI270521v1': 7642, 'chrUn_GL000195v1': 182896, 'chrUn_GL000219v1': 179198, 'chrUn_GL000220v1': 161802, 'chrUn_GL000224v1': 179693, 'chrUn_KI270741v1': 157432, 'chrUn_GL000226v1': 15008, 'chrUn_GL000213v1': 164239, 'chrUn_KI270743v1': 210658, 'chrUn_KI270744v1': 168472, 'chrUn_KI270745v1': 41891, 'chrUn_KI270746v1': 66486, 'chrUn_KI270747v1': 198735, 'chrUn_KI270748v1': 93321, 'chrUn_KI270749v1': 158759, 'chrUn_KI270750v1': 148850, 'chrUn_KI270751v1': 150742, 'chrUn_KI270752v1': 27745, 'chrUn_KI270753v1': 62944, 'chrUn_KI270754v1': 40191, 'chrUn_KI270755v1': 36723, 'chrUn_KI270756v1': 79590, 'chrUn_KI270757v1': 71251, 'chrUn_GL000214v1': 137718, 'chrUn_KI270742v1': 186739, 'chrUn_GL000216v2': 176608, 'chrUn_GL000218v1': 161147, 'chrEBV': 171823}\n", - "\tContig chr17\n", - "16 total jobs\n", - "chr17:011, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:005, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:012, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:010, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:001, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:004, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:009, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:015, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:002, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:007, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:013, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:006, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:014, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "Reads processed:\t1\n", - "Time to process reads in min:\t0.02508\n", - "Summary:\t chr17\n", - "edited 1\n", - "\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Calculating coverage at edited sites, minimum read quality is 0...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "\tsplit chr17_000_0_5203591, 0/16...\n", - "\tsplit chr17_010_52035910_57239501, 10/16...\n", - "Done grouping! Concatenating ...\n", - "Done concatenating!\n", - "edit_info_grouped_per_contig_combined dict_keys(['chr17_000_0_5203591', 'chr17_001_5203591_10407182', 'chr17_002_10407182_15610773', 'chr17_003_15610773_20814364', 'chr17_004_20814364_26017955', 'chr17_005_26017955_31221546', 'chr17_006_31221546_36425137', 'chr17_007_36425137_41628728', 'chr17_008_41628728_46832319', 'chr17_009_46832319_52035910', 'chr17_010_52035910_57239501', 'chr17_011_57239501_62443092', 'chr17_012_62443092_67646683', 'chr17_013_67646683_72850274', 'chr17_014_72850274_78053865', 'chr17_015_78053865_83257456'])\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "100%|██████████| 16/16 [00:01<00:00, 11.56it/s]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/F2R1_end_second_in_pair_test/split_bams/chr17/chr17_008_41628728_46832319.bam.sorted.bam\n", - " chr17:43001715~~~~~~~`\n", - "coverage_at_pos 1\n", - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/F2R1_end_second_in_pair_test/split_bams/chr17/chr17_008_41628728_46832319.bam.sorted.bam\n", - " chr17:43001716~~~~~~~`\n", - "coverage_at_pos 1\n", - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/F2R1_end_second_in_pair_test/split_bams/chr17/chr17_008_41628728_46832319.bam.sorted.bam\n", - " chr17:43001717~~~~~~~`\n", - "coverage_at_pos 1\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "100%|██████████| 16/16 [00:01<00:00, 11.61it/s]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Concatenating results...\n", - "Done concatenating.\n", - "Total time to calculate coverage: 0.024 minutes\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Filtering and calculating site-level statistics\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Loading edit information...\n", - "Filtering..\n", - "~~~~~~~~~~~~~~~~~~~~~~~\n", - "Filtering edited sites\n", - "~~~~~~~~~~~~~~~~~~~~~~~\n", - "Minimum distance from end = 0, Minimum base-calling quality = 0\n", - "Deduplicating....\n", - "\tNumber of edits before filtering:\n", - "\t3\n", - "\tNumber of edits after filtering:\n", - "\t3\n", - "\tNumber of edits after deduplicating:\n", - "\t3\n", - "\tNumber of unique edit sites:\n", - "\t3\n", - "Writing sites...\n", - "\n", - "Adding strand-specific conversion...\n", - "\n", - "3 sites being converted to SAILOR format...\n", - "0 rows had coverage of 0 or more edits than coverage... filtering these out, but look into them...\n", - "0 final deduplicated SAILOR-formatted sites\n", - "Annotating sites with GTF information from /tscc/projects/ps-yeolab3/ekofman/sailor2//annotations/hg38_gencode.v35.annotation.genes.bed...\n", - "Current memory usage 21.514482MB; Peak: 22.624894MB\n", - "Time elapsed: 4.16s\n", - "++++++\n", - "Done!\n", - "++++++\n", - "same_pos_dif_reads_test\n", - "Removing old files...\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "rm: cannot remove 'tests/strandedness_tests/same_pos_dif_reads_test/*': No such file or directory\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Running tests...\n", - "Assuming 16 cores available for multiprocessing. Set this to the number of available cores for optimal execution.\n", - "Arguments:\n", - "\tBAM filepath:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/bams/same_pos_dif_reads.bam\n", - "\tAnnotation bedfile filepath:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//annotations/hg38_gencode.v35.annotation.genes.bed\n", - "\tOutput folder:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/same_pos_dif_reads_test\n", - "\tBarcode whitelist:\tNone\n", - "\tStrandedness:\t2\n", - "\tBarcode Tag:\tNone\n", - "\tPaired End:\tTrue\n", - "\tCoverage only:\tFalse\n", - "\tFiltering only:\tFalse\n", - "\tAnnotation only:\tFalse\n", - "\tSailor outputs:\tTrue\n", - "\tMinimum base quality:\t0\n", - "\tMinimum read quality:\t0\n", - "\tMinimum distance from end:\t0\n", - "\tmax_edits_per_read:\tNone\n", - "\tContigs:\tchr17\n", - "\tNumber of intervals:\t16\n", - "\tCores:\t16\n", - "\tVerbose:\tTrue\n", - "\tSkip coverage?:\tFalse\n", - "\n", - ":::: :::: ::: ::::::::: ::::::::::: :::: ::: :::::::::: \n", - "+:+:+: :+:+:+ :+: :+: :+: :+: :+: :+:+: :+: :+: \n", - "+:+ +:+:+ +:+ +:+ +:+ +:+ +:+ +:+ :+:+:+ +:+ +:+ \n", - "+#+ +:+ +#+ +#++:++#++: +#++:++#: +#+ +#+ +:+ +#+ +#++:++# \n", - "+#+ +#+ +#+ +#+ +#+ +#+ +#+ +#+ +#+#+# +#+ \n", - "#+# #+# #+# #+# #+# #+# #+# #+# #+#+# #+# \n", - "### ### ### ### ### ### ########### ### #### ########## \n", - "==================================================================\n", - "Multi-core Algorithm for Rapid Identification of Nucleotide Edits\n", - "==================================================================\n", - "~~~~~~~~~~~~~~~~~~\n", - "Identifying edits\n", - "~~~~~~~~~~~~~~~~~~\n", - "Each contig is being split into 16 subsets...\n", - "contig_lengths_dict:{'chr1': 248956422, 'chr2': 242193529, 'chr3': 198295559, 'chr4': 190214555, 'chr5': 181538259, 'chr6': 170805979, 'chr7': 159345973, 'chr8': 145138636, 'chr9': 138394717, 'chr10': 133797422, 'chr11': 135086622, 'chr12': 133275309, 'chr13': 114364328, 'chr14': 107043718, 'chr15': 101991189, 'chr16': 90338345, 'chr17': 83257441, 'chr18': 80373285, 'chr19': 58617616, 'chr20': 64444167, 'chr21': 46709983, 'chr22': 50818468, 'chrX': 156040895, 'chrY': 57227415, 'chrM': 16569, 'chr1_KI270706v1_random': 175055, 'chr1_KI270707v1_random': 32032, 'chr1_KI270708v1_random': 127682, 'chr1_KI270709v1_random': 66860, 'chr1_KI270710v1_random': 40176, 'chr1_KI270711v1_random': 42210, 'chr1_KI270712v1_random': 176043, 'chr1_KI270713v1_random': 40745, 'chr1_KI270714v1_random': 41717, 'chr2_KI270715v1_random': 161471, 'chr2_KI270716v1_random': 153799, 'chr3_GL000221v1_random': 155397, 'chr4_GL000008v2_random': 209709, 'chr5_GL000208v1_random': 92689, 'chr9_KI270717v1_random': 40062, 'chr9_KI270718v1_random': 38054, 'chr9_KI270719v1_random': 176845, 'chr9_KI270720v1_random': 39050, 'chr11_KI270721v1_random': 100316, 'chr14_GL000009v2_random': 201709, 'chr14_GL000225v1_random': 211173, 'chr14_KI270722v1_random': 194050, 'chr14_GL000194v1_random': 191469, 'chr14_KI270723v1_random': 38115, 'chr14_KI270724v1_random': 39555, 'chr14_KI270725v1_random': 172810, 'chr14_KI270726v1_random': 43739, 'chr15_KI270727v1_random': 448248, 'chr16_KI270728v1_random': 1872759, 'chr17_GL000205v2_random': 185591, 'chr17_KI270729v1_random': 280839, 'chr17_KI270730v1_random': 112551, 'chr22_KI270731v1_random': 150754, 'chr22_KI270732v1_random': 41543, 'chr22_KI270733v1_random': 179772, 'chr22_KI270734v1_random': 165050, 'chr22_KI270735v1_random': 42811, 'chr22_KI270736v1_random': 181920, 'chr22_KI270737v1_random': 103838, 'chr22_KI270738v1_random': 99375, 'chr22_KI270739v1_random': 73985, 'chrY_KI270740v1_random': 37240, 'chrUn_KI270302v1': 2274, 'chrUn_KI270304v1': 2165, 'chrUn_KI270303v1': 1942, 'chrUn_KI270305v1': 1472, 'chrUn_KI270322v1': 21476, 'chrUn_KI270320v1': 4416, 'chrUn_KI270310v1': 1201, 'chrUn_KI270316v1': 1444, 'chrUn_KI270315v1': 2276, 'chrUn_KI270312v1': 998, 'chrUn_KI270311v1': 12399, 'chrUn_KI270317v1': 37690, 'chrUn_KI270412v1': 1179, 'chrUn_KI270411v1': 2646, 'chrUn_KI270414v1': 2489, 'chrUn_KI270419v1': 1029, 'chrUn_KI270418v1': 2145, 'chrUn_KI270420v1': 2321, 'chrUn_KI270424v1': 2140, 'chrUn_KI270417v1': 2043, 'chrUn_KI270422v1': 1445, 'chrUn_KI270423v1': 981, 'chrUn_KI270425v1': 1884, 'chrUn_KI270429v1': 1361, 'chrUn_KI270442v1': 392061, 'chrUn_KI270466v1': 1233, 'chrUn_KI270465v1': 1774, 'chrUn_KI270467v1': 3920, 'chrUn_KI270435v1': 92983, 'chrUn_KI270438v1': 112505, 'chrUn_KI270468v1': 4055, 'chrUn_KI270510v1': 2415, 'chrUn_KI270509v1': 2318, 'chrUn_KI270518v1': 2186, 'chrUn_KI270508v1': 1951, 'chrUn_KI270516v1': 1300, 'chrUn_KI270512v1': 22689, 'chrUn_KI270519v1': 138126, 'chrUn_KI270522v1': 5674, 'chrUn_KI270511v1': 8127, 'chrUn_KI270515v1': 6361, 'chrUn_KI270507v1': 5353, 'chrUn_KI270517v1': 3253, 'chrUn_KI270529v1': 1899, 'chrUn_KI270528v1': 2983, 'chrUn_KI270530v1': 2168, 'chrUn_KI270539v1': 993, 'chrUn_KI270538v1': 91309, 'chrUn_KI270544v1': 1202, 'chrUn_KI270548v1': 1599, 'chrUn_KI270583v1': 1400, 'chrUn_KI270587v1': 2969, 'chrUn_KI270580v1': 1553, 'chrUn_KI270581v1': 7046, 'chrUn_KI270579v1': 31033, 'chrUn_KI270589v1': 44474, 'chrUn_KI270590v1': 4685, 'chrUn_KI270584v1': 4513, 'chrUn_KI270582v1': 6504, 'chrUn_KI270588v1': 6158, 'chrUn_KI270593v1': 3041, 'chrUn_KI270591v1': 5796, 'chrUn_KI270330v1': 1652, 'chrUn_KI270329v1': 1040, 'chrUn_KI270334v1': 1368, 'chrUn_KI270333v1': 2699, 'chrUn_KI270335v1': 1048, 'chrUn_KI270338v1': 1428, 'chrUn_KI270340v1': 1428, 'chrUn_KI270336v1': 1026, 'chrUn_KI270337v1': 1121, 'chrUn_KI270363v1': 1803, 'chrUn_KI270364v1': 2855, 'chrUn_KI270362v1': 3530, 'chrUn_KI270366v1': 8320, 'chrUn_KI270378v1': 1048, 'chrUn_KI270379v1': 1045, 'chrUn_KI270389v1': 1298, 'chrUn_KI270390v1': 2387, 'chrUn_KI270387v1': 1537, 'chrUn_KI270395v1': 1143, 'chrUn_KI270396v1': 1880, 'chrUn_KI270388v1': 1216, 'chrUn_KI270394v1': 970, 'chrUn_KI270386v1': 1788, 'chrUn_KI270391v1': 1484, 'chrUn_KI270383v1': 1750, 'chrUn_KI270393v1': 1308, 'chrUn_KI270384v1': 1658, 'chrUn_KI270392v1': 971, 'chrUn_KI270381v1': 1930, 'chrUn_KI270385v1': 990, 'chrUn_KI270382v1': 4215, 'chrUn_KI270376v1': 1136, 'chrUn_KI270374v1': 2656, 'chrUn_KI270372v1': 1650, 'chrUn_KI270373v1': 1451, 'chrUn_KI270375v1': 2378, 'chrUn_KI270371v1': 2805, 'chrUn_KI270448v1': 7992, 'chrUn_KI270521v1': 7642, 'chrUn_GL000195v1': 182896, 'chrUn_GL000219v1': 179198, 'chrUn_GL000220v1': 161802, 'chrUn_GL000224v1': 179693, 'chrUn_KI270741v1': 157432, 'chrUn_GL000226v1': 15008, 'chrUn_GL000213v1': 164239, 'chrUn_KI270743v1': 210658, 'chrUn_KI270744v1': 168472, 'chrUn_KI270745v1': 41891, 'chrUn_KI270746v1': 66486, 'chrUn_KI270747v1': 198735, 'chrUn_KI270748v1': 93321, 'chrUn_KI270749v1': 158759, 'chrUn_KI270750v1': 148850, 'chrUn_KI270751v1': 150742, 'chrUn_KI270752v1': 27745, 'chrUn_KI270753v1': 62944, 'chrUn_KI270754v1': 40191, 'chrUn_KI270755v1': 36723, 'chrUn_KI270756v1': 79590, 'chrUn_KI270757v1': 71251, 'chrUn_GL000214v1': 137718, 'chrUn_KI270742v1': 186739, 'chrUn_GL000216v2': 176608, 'chrUn_GL000218v1': 161147, 'chrEBV': 171823}\n", - "\tContig chr17\n", - "16 total jobs\n", - "chr17:000, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:005, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:010, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 55C43\n", - "CIGAR tag 1S97M17144N2M\n", - "is_reverse False\n", - "is_read1 False\n", - "is_read2 True\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse True\n", - "read id VH01429:22:AACFJ5NHV:2:2606:39477:40189\n", - "VH01429:22:AACFJ5NHV:2:2606:39477:40189\t163\t#16\t83195127\t255\t1S97M17144N2M\t#16\t83195141\t17258\tTCCCACCTTCGCTTCCGGGACCACAGAGCCCCTGGAGCCTGCACGCCACGGAGTCTACCACTGAGGAGTGAGGAGGCCTCTTGTGGGGACAGATCTGGGA\tarray('B', [34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 12, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34])\t[('MD', '55C43'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 1), ('AS', 197), ('XS', '+')]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 55C43\n", - "CIGAR string 1S97M17144N2M\n", - "Reference seq: CCCACCTTCGCTTCCGGGACCACAGAGCCCCTGGAGCCTGCACGCCACGGAGTCTCCCACTGAGGAGTGAGGAGGCCTCTTGTGGGGACAGATCTGGGA\n", - "Aligned seq: TCCCACCTTCGCTTCCGGGACCACAGAGCCCCTGGAGCCTGCACGCCACGGAGTCTACCACTGAGGAGTGAGGAGGCCTCTTGTGGGGACAGATCTGGGA\n", - "Qualities: array('B', [34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 12, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 1), (0, 97), (3, 17144), (0, 2)]\n", - "Aligned sequence before clipping (if needed):\n", - " TCCCACCTTCGCTTCCGGGACCACAGAGCCCCTGGAGCCTGCACGCCACGGAGTCTACCACTGAGGAGTGAGGAGGCCTCTTGTGGGGACAGATCTGGGA\n", - "Qualities before clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 12, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 97), (3, 17144), (0, 2)]\n", - "Aligned sequence after clipping (if needed):\n", - " CCCACCTTCGCTTCCGGGACCACAGAGCCCCTGGAGCCTGCACGCCACGGAGTCTACCACTGAGGAGTGAGGAGGCCTCTTGTGGGGACAGATCTGGGA\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 12, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['55', '43']\n", - "[55, 99]\n", - "Indicated reference seq:\n", - " cccaccttcgcttccgggaccacagagcccctggagcctgcacgccacggagtctCccactgaggagtgaggaggcctcttgtggggacagatctggga\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " cccaccttcgcttccgggaccacagagcccctggagcctgcacgccacggagtctCccactgaggagtgaggaggcctcttgtggggacagatctgg17144*nga\n", - "Fixed aligned seq:\n", - " CCCACCTTCGCTTCCGGGACCACAGAGCCCCTGGAGCCTGCACGCCACGGAGTCTACCACTGAGGAGTGAGGAGGCCTCTTGTGGGGACAGATCTGG17144*nGA\n", - "Finalized fixed aligned seq:\n", - " cccaccttcgcttccgggaccacagagcccctggagcctgcacgccacggagtctAccactgaggagtgaggaggcctcttgtggggacagatctgg17144*nga\n", - "Indicated qualities:\n", - " 343434343434342626343434343434343434343434263434263434343434343434343434343434263434343434343434343434343434341234341234343426343434343434343434343434343434343434343434343434263434343434343412343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['A']\n", - "ref bases ['C']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['A'], ref bases: ['C']\n", - "Getting info: A C 12 56\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 86C13\n", - "CIGAR tag 1S17M4579N83M\n", - "is_reverse False\n", - "is_read1 False\n", - "is_read2 True\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse True\n", - "read id VH01429:22:AACFJ5NHV:2:1602:67558:13893\n", - "VH01429:22:AACFJ5NHV:2:1602:67558:13893\t163\t#16\t83195207\t255\t1S17M4579N83M\t#16\t83199866\t4757\tGTGTGGGGACAGATCTGGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAAT\tarray('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\t[('MD', '86C13'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 1), ('AS', 191), ('XS', '+')]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 86C13\n", - "CIGAR string 1S17M4579N83M\n", - "Reference seq: TGTGGGGACAGATCTGGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTCTGTGGCGATTAAT\n", - "Aligned seq: GTGTGGGGACAGATCTGGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAAT\n", - "Qualities: array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 1), (0, 17), (3, 4579), (0, 83)]\n", - "Aligned sequence before clipping (if needed):\n", - " GTGTGGGGACAGATCTGGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAAT\n", - "Qualities before clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 17), (3, 4579), (0, 83)]\n", - "Aligned sequence after clipping (if needed):\n", - " TGTGGGGACAGATCTGGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAAT\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['86', '13']\n", - "[86, 100]\n", - "Indicated reference seq:\n", - " tgtggggacagatctggaatgagtggcatccaaacctgactcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaat\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " tgtggggacagatctgg4579*naatgagtggcatccaaacctgactcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaat\n", - "Fixed aligned seq:\n", - " TGTGGGGACAGATCTGG4579*nAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAAT\n", - "Finalized fixed aligned seq:\n", - " tgtggggacagatctgg4579*naatgagtggcatccaaacctgactcatatttccaactttattaatttttgcaagacttcggagggtgctGtgtggcgattaat\n", - "Indicated qualities:\n", - " 34343434343434343434342634342634343434343434343434343434343434343434343434343412343434343434343434343434343434343434343434343434343434343434341234343434343434343434343426343434343434343434343434343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['G']\n", - "ref bases ['C']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['G'], ref bases: ['C']\n", - "Getting info: G C 34 4666\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 95C4\n", - "CIGAR tag 1S100M\n", - "is_reverse False\n", - "is_read1 False\n", - "is_read2 True\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse True\n", - "read id VH01429:22:AACFJ5NHV:1:1109:44703:39053\n", - "VH01429:22:AACFJ5NHV:1:1109:44703:39053\t163\t#16\t83199777\t255\t1S100M\t#16\t83199839\t163\tGCTATTATTGAGTTTCTTCTTTTTCAGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTG\tarray('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34])\t[('MD', '95C4'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 1), ('AS', 191)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 95C4\n", - "CIGAR string 1S100M\n", - "Reference seq: CTATTATTGAGTTTCTTCTTTTTCAGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTCTGTG\n", - "Aligned seq: GCTATTATTGAGTTTCTTCTTTTTCAGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTG\n", - "Qualities: array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 1), (0, 100)]\n", - "Aligned sequence before clipping (if needed):\n", - " GCTATTATTGAGTTTCTTCTTTTTCAGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTG\n", - "Qualities before clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 100)]\n", - "Aligned sequence after clipping (if needed):\n", - " CTATTATTGAGTTTCTTCTTTTTCAGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTG\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['95', '4']\n", - "[95, 100]\n", - "Indicated reference seq:\n", - " ctattattgagtttcttctttttcagaatgagtggcatccaaacctgactcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtg\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " ctattattgagtttcttctttttcagaatgagtggcatccaaacctgactcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtg\n", - "Fixed aligned seq:\n", - " CTATTATTGAGTTTCTTCTTTTTCAGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTG\n", - "Finalized fixed aligned seq:\n", - " ctattattgagtttcttctttttcagaatgagtggcatccaaacctgactcatatttccaactttattaatttttgcaagacttcggagggtgctGtgtg\n", - "Indicated qualities:\n", - " 34343434343434343434343434343434123434343434343434343434343434343434343434343434343426343434343434343434343434343434343434342634343434343426343434343434343434343434343434343434343434343426343434343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['G']\n", - "ref bases ['C']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['G'], ref bases: ['C']\n", - "Getting info: G C 34 96\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 92C8\n", - "CIGAR tag 101M\n", - "is_reverse True\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id VH01429:22:AACFJ5NHV:2:1208:38151:26028\n", - "VH01429:22:AACFJ5NHV:2:1208:38151:26028\t83\t#16\t83199780\t255\t101M\t#16\t83199711\t-170\tTTATTGAGTTTCTTCTTTTTCAGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGA\tarray('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26])\t[('MD', '92C8'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 1), ('AS', 195)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 92C8\n", - "CIGAR string 101M\n", - "Reference seq: TTATTGAGTTTCTTCTTTTTCAGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTCTGTGGCGA\n", - "Aligned seq: TTATTGAGTTTCTTCTTTTTCAGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGA\n", - "Qualities: array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(0, 101)]\n", - "Aligned sequence before clipping (if needed):\n", - " TTATTGAGTTTCTTCTTTTTCAGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGA\n", - "Qualities before clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 101)]\n", - "Aligned sequence after clipping (if needed):\n", - " TTATTGAGTTTCTTCTTTTTCAGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGA\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['92', '8']\n", - "[92, 101]\n", - "Indicated reference seq:\n", - " ttattgagtttcttctttttcagaatgagtggcatccaaacctgactcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcga\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " ttattgagtttcttctttttcagaatgagtggcatccaaacctgactcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcga\n", - "Fixed aligned seq:\n", - " TTATTGAGTTTCTTCTTTTTCAGAATGAGTGGCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGA\n", - "Finalized fixed aligned seq:\n", - " ttattgagtttcttctttttcagaatgagtggcatccaaacctgactcatatttccaactttattaatttttgcaagacttcggagggtgctGtgtggcga\n", - "Indicated qualities:\n", - " 3434343434343434343426343426343434343434343426343434343434343434343434343434343434343434343434343434343434343434343434263434343434343426343434343434343434343434343434343434343434343434343434343426343426\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['G']\n", - "ref bases ['C']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['G'], ref bases: ['C']\n", - "Getting info: G C 34 93\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 60C37\n", - "CIGAR tag 1S98M2S\n", - "is_reverse False\n", - "is_read1 False\n", - "is_read2 True\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse True\n", - "read id VH01429:22:AACFJ5NHV:1:2112:47146:35399\n", - "VH01429:22:AACFJ5NHV:1:2112:47146:35399\t163\t#16\t83199812\t255\t1S98M2S\t#16\t83199946\t232\tTCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAAT\tarray('B', [34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\t[('MD', '60C37'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 1), ('AS', 192)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 60C37\n", - "CIGAR string 1S98M2S\n", - "Reference seq: CATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTCTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCA\n", - "Aligned seq: TCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAAT\n", - "Qualities: array('B', [34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 1), (0, 98), (4, 2)]\n", - "Aligned sequence before clipping (if needed):\n", - " TCATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAAT\n", - "Qualities before clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 98)]\n", - "Aligned sequence after clipping (if needed):\n", - " CATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCA\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['60', '37']\n", - "[60, 98]\n", - "Indicated reference seq:\n", - " catccaaacctgactcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgca\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " catccaaacctgactcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgca\n", - "Fixed aligned seq:\n", - " CATCCAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCA\n", - "Finalized fixed aligned seq:\n", - " catccaaacctgactcatatttccaactttattaatttttgcaagacttcggagggtgctGtgtggcgattaatattgctgagctgagcacagctgca\n", - "Indicated qualities:\n", - " 3434343434343426343434343434343434343434343434342634343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['G']\n", - "ref bases ['C']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['G'], ref bases: ['C']\n", - "Getting info: G C 34 61\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 5C50C37G5\n", - "CIGAR tag 1S100M\n", - "is_reverse False\n", - "is_read1 False\n", - "is_read2 True\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse True\n", - "read id VH01429:22:AACFJ5NHV:2:2610:69319:26899\n", - "VH01429:22:AACFJ5NHV:2:2610:69319:26899\t163\t#16\t83199816\t255\t1S100M\t#16\t83199822\t105\tTCAAACTTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTT\tarray('B', [34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 26, 34, 34, 34, 12, 34, 34, 12, 34, 12, 26, 26, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26])\t[('MD', '5C50C37G5'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 3), ('AS', 187)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 5C50C37G5\n", - "CIGAR string 1S100M\n", - "Reference seq: CAAACCTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTCTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAGTACTT\n", - "Aligned seq: TCAAACTTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTT\n", - "Qualities: array('B', [34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 26, 34, 34, 34, 12, 34, 34, 12, 34, 12, 26, 26, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 1), (0, 100)]\n", - "Aligned sequence before clipping (if needed):\n", - " TCAAACTTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTT\n", - "Qualities before clipping:\n", - " array('B', [34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 26, 34, 34, 34, 12, 34, 34, 12, 34, 12, 26, 26, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 100)]\n", - "Aligned sequence after clipping (if needed):\n", - " CAAACTTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTT\n", - "Qualities after clipping:\n", - " array('B', [26, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 26, 34, 34, 34, 12, 34, 34, 12, 34, 12, 26, 26, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['5', '50', '37', '5']\n", - "[5, 56, 94, 100]\n", - "Indicated reference seq:\n", - " caaacCtgactcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactt\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " caaacCtgactcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactt\n", - "Fixed aligned seq:\n", - " CAAACTTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTT\n", - "Finalized fixed aligned seq:\n", - " caaacTtgactcatatttccaactttattaatttttgcaagacttcggagggtgctGtgtggcgattaatattgctgagctgagcacagctgcaAtactt\n", - "Indicated qualities:\n", - " 26343434343434343412342634343412343412341226263434343434341234343434343434343434123434343434343434343434343434343434343434342634343434343412343434343434263434343434343434343434343434343434343434342626\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['T', 'G', 'A']\n", - "ref bases ['C', 'C', 'G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['T', 'G', 'A'], ref bases: ['C', 'C', 'G']\n", - "Getting info: T C 34 6\n", - "Getting info: G C 34 57\n", - "Getting info: A G 34 95\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 50C37G10\n", - "CIGAR tag 1S99M1S\n", - "is_reverse True\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id VH01429:22:AACFJ5NHV:2:2610:69319:26899\n", - "VH01429:22:AACFJ5NHV:2:2610:69319:26899\t83\t#16\t83199822\t255\t1S99M1S\t#16\t83199816\t-105\tTTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGA\tarray('B', [34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 26, 26, 34, 34, 12, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 26, 34, 34, 26, 34, 34, 12, 34, 12, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\t[('MD', '50C37G10'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 2), ('AS', 187)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 50C37G10\n", - "CIGAR string 1S99M1S\n", - "Reference seq: TGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTCTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAGTACTTTCCTG\n", - "Aligned seq: TTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGA\n", - "Qualities: array('B', [34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 26, 26, 34, 34, 12, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 26, 34, 34, 26, 34, 34, 12, 34, 12, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 1), (0, 99), (4, 1)]\n", - "Aligned sequence before clipping (if needed):\n", - " TTGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGA\n", - "Qualities before clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 26, 26, 34, 34, 12, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 26, 34, 34, 26, 34, 34, 12, 34, 12, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 99)]\n", - "Aligned sequence after clipping (if needed):\n", - " TGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTG\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 12, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 26, 26, 34, 34, 12, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 26, 34, 34, 26, 34, 34, 12, 34, 12, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['50', '37', '10']\n", - "[50, 88, 99]\n", - "Indicated reference seq:\n", - " tgactcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctg\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " tgactcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctg\n", - "Fixed aligned seq:\n", - " TGACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTG\n", - "Finalized fixed aligned seq:\n", - " tgactcatatttccaactttattaatttttgcaagacttcggagggtgctGtgtggcgattaatattgctgagctgagcacagctgcaAtactttcctg\n", - "Indicated qualities:\n", - " 343434343434341234123434343434343434343434343434343434343412343426263434121234343434343434343434343434343412342634342634341234123434343434341234343434343434343434343434343434343434343434343434343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['G', 'A']\n", - "ref bases ['C', 'G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['G', 'A'], ref bases: ['C', 'G']\n", - "Getting info: G C 34 51\n", - "Getting info: A G 34 89\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 48C37G14\n", - "CIGAR tag 101M\n", - "is_reverse True\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id VH01429:22:AACFJ5NHV:1:1403:49513:32843\n", - "VH01429:22:AACFJ5NHV:1:1403:49513:32843\t83\t#16\t83199824\t255\t101M\t#16\t83199748\t-177\tACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAA\tarray('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\t[('MD', '48C37G14'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 2), ('AS', 194)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 48C37G14\n", - "CIGAR string 101M\n", - "Reference seq: ACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTCTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAGTACTTTCCTGTAAA\n", - "Aligned seq: ACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAA\n", - "Qualities: array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(0, 101)]\n", - "Aligned sequence before clipping (if needed):\n", - " ACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAA\n", - "Qualities before clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 101)]\n", - "Aligned sequence after clipping (if needed):\n", - " ACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAA\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['48', '37', '14']\n", - "[48, 86, 101]\n", - "Indicated reference seq:\n", - " actcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaa\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " actcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaa\n", - "Fixed aligned seq:\n", - " ACTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAA\n", - "Finalized fixed aligned seq:\n", - " actcatatttccaactttattaatttttgcaagacttcggagggtgctGtgtggcgattaatattgctgagctgagcacagctgcaAtactttcctgtaaa\n", - "Indicated qualities:\n", - " 3434343434343434343434343434341234123434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['G', 'A']\n", - "ref bases ['C', 'G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['G', 'A'], ref bases: ['C', 'G']\n", - "Getting info: G C 34 49\n", - "Getting info: A G 34 87\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 47C37G14\n", - "CIGAR tag 1S100M\n", - "is_reverse False\n", - "is_read1 False\n", - "is_read2 True\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse True\n", - "read id VH01429:22:AACFJ5NHV:1:2414:26942:20235\n", - "VH01429:22:AACFJ5NHV:1:2414:26942:20235\t163\t#16\t83199825\t255\t1S100M\t#16\t83199839\t115\tTCTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAA\tarray('B', [34, 12, 34, 34, 34, 12, 34, 34, 26, 34, 34, 34, 34, 12, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 26, 34, 12, 34, 12, 26, 12, 34, 34, 26, 12, 34, 34, 34, 34, 26, 34, 34, 26, 34, 26, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34])\t[('MD', '47C37G14'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 2), ('AS', 191)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 47C37G14\n", - "CIGAR string 1S100M\n", - "Reference seq: CTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTCTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAGTACTTTCCTGTAAA\n", - "Aligned seq: TCTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAA\n", - "Qualities: array('B', [34, 12, 34, 34, 34, 12, 34, 34, 26, 34, 34, 34, 34, 12, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 26, 34, 12, 34, 12, 26, 12, 34, 34, 26, 12, 34, 34, 34, 34, 26, 34, 34, 26, 34, 26, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 1), (0, 100)]\n", - "Aligned sequence before clipping (if needed):\n", - " TCTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAA\n", - "Qualities before clipping:\n", - " array('B', [34, 12, 34, 34, 34, 12, 34, 34, 26, 34, 34, 34, 34, 12, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 26, 34, 12, 34, 12, 26, 12, 34, 34, 26, 12, 34, 34, 34, 34, 26, 34, 34, 26, 34, 26, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 100)]\n", - "Aligned sequence after clipping (if needed):\n", - " CTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAA\n", - "Qualities after clipping:\n", - " array('B', [12, 34, 34, 34, 12, 34, 34, 26, 34, 34, 34, 34, 12, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 26, 34, 34, 26, 34, 12, 34, 12, 26, 12, 34, 34, 26, 12, 34, 34, 34, 34, 26, 34, 34, 26, 34, 26, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['47', '37', '14']\n", - "[47, 85, 100]\n", - "Indicated reference seq:\n", - " ctcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaa\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " ctcatatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaa\n", - "Fixed aligned seq:\n", - " CTCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAA\n", - "Finalized fixed aligned seq:\n", - " ctcatatttccaactttattaatttttgcaagacttcggagggtgctGtgtggcgattaatattgctgagctgagcacagctgcaAtactttcctgtaaa\n", - "Indicated qualities:\n", - " 12343434123434263434343412343434263434343434343434343434343434123434343426343426343434343434343434341226343434343434343434263434263434263412341226123434261234343434263434263426343434341234343434343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['G', 'A']\n", - "ref bases ['C', 'G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['G', 'A'], ref bases: ['C', 'G']\n", - "Getting info: G C 34 48\n", - "Getting info: A G 26 86\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 2T9T0T26G4C37G1A11\n", - "CIGAR tag 3S97M\n", - "is_reverse False\n", - "is_read1 False\n", - "is_read2 True\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse True\n", - "read id VH01429:22:AACFJ5NHV:2:1608:28097:17679\n", - "VH01429:22:AACFJ5NHV:2:1608:28097:17679\t163\t#16\t83199827\t255\t3S97M\t#16\t83199827\t100\tCCACAAATTTCCAACAATATTAATTTTTGCAAGACTTCGGAGGCTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATTCTTTCCTGTAA\tarray('B', [12, 12, 12, 12, 12, 12, 34, 12, 34, 34, 34, 12, 34, 34, 12, 12, 12, 34, 34, 34, 12, 12, 34, 12, 12, 34, 12, 12, 34, 34, 34, 34, 26, 34, 34, 12, 26, 34, 12, 34, 26, 34, 12, 12, 34, 34, 34, 34, 34, 12, 12, 26, 26, 34, 34, 34, 34, 34, 34, 26, 34, 34, 12, 34, 12, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34])\t[('MD', '2T9T0T26G4C37G1A11'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 7), ('AS', 177)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 2T9T0T26G4C37G1A11\n", - "CIGAR string 3S97M\n", - "Reference seq: CATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTCTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAGTACTTTCCTGTAA\n", - "Aligned seq: CCACAAATTTCCAACAATATTAATTTTTGCAAGACTTCGGAGGCTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATTCTTTCCTGTAA\n", - "Qualities: array('B', [12, 12, 12, 12, 12, 12, 34, 12, 34, 34, 34, 12, 34, 34, 12, 12, 12, 34, 34, 34, 12, 12, 34, 12, 12, 34, 12, 12, 34, 34, 34, 34, 26, 34, 34, 12, 26, 34, 12, 34, 26, 34, 12, 12, 34, 34, 34, 34, 34, 12, 12, 26, 26, 34, 34, 34, 34, 34, 34, 26, 34, 34, 12, 34, 12, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 3), (0, 97)]\n", - "Aligned sequence before clipping (if needed):\n", - " CCACAAATTTCCAACAATATTAATTTTTGCAAGACTTCGGAGGCTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATTCTTTCCTGTAA\n", - "Qualities before clipping:\n", - " array('B', [12, 12, 12, 12, 12, 12, 34, 12, 34, 34, 34, 12, 34, 34, 12, 12, 12, 34, 34, 34, 12, 12, 34, 12, 12, 34, 12, 12, 34, 34, 34, 34, 26, 34, 34, 12, 26, 34, 12, 34, 26, 34, 12, 12, 34, 34, 34, 34, 34, 12, 12, 26, 26, 34, 34, 34, 34, 34, 34, 26, 34, 34, 12, 34, 12, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 97)]\n", - "Aligned sequence after clipping (if needed):\n", - " CAAATTTCCAACAATATTAATTTTTGCAAGACTTCGGAGGCTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATTCTTTCCTGTAA\n", - "Qualities after clipping:\n", - " array('B', [12, 12, 12, 34, 12, 34, 34, 34, 12, 34, 34, 12, 12, 12, 34, 34, 34, 12, 12, 34, 12, 12, 34, 12, 12, 34, 34, 34, 34, 26, 34, 34, 12, 26, 34, 12, 34, 26, 34, 12, 12, 34, 34, 34, 34, 34, 12, 12, 26, 26, 34, 34, 34, 34, 34, 34, 26, 34, 34, 12, 34, 12, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['2', '9', '0', '26', '4', '37', '1', '11']\n", - "[2, 12, 13, 40, 45, 83, 85, 97]\n", - "Indicated reference seq:\n", - " caTatttccaacTTtattaatttttgcaagacttcggaggGtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtActttcctgtaa\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " caTatttccaacTTtattaatttttgcaagacttcggaggGtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtActttcctgtaa\n", - "Fixed aligned seq:\n", - " CAAATTTCCAACAATATTAATTTTTGCAAGACTTCGGAGGCTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATTCTTTCCTGTAA\n", - "Finalized fixed aligned seq:\n", - " caAatttccaacAAtattaatttttgcaagacttcggaggCtgctGtgtggcgattaatattgctgagctgagcacagctgcaAtTctttcctgtaa\n", - "Indicated qualities:\n", - " 12121234123434341234341212123434341212341212341212343434342634341226341234263412123434343434121226263434343434342634341234122634343434343434343412343434343434343434343434123434342634343434343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['A', 'A', 'A', 'C', 'G', 'A', 'T']\n", - "ref bases ['T', 'T', 'T', 'G', 'C', 'G', 'A']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['A', 'A', 'A', 'C', 'G', 'A', 'T'], ref bases: ['T', 'T', 'T', 'G', 'C', 'G', 'A']\n", - "Getting info: A T 12 3\n", - "Getting info: A T 12 13\n", - "Getting info: A T 12 14\n", - "Getting info: C G 12 41\n", - "Getting info: G C 34 46\n", - "Getting info: A G 34 84\n", - "Getting info: T A 12 86\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 45C37G16\n", - "CIGAR tag 100M1S\n", - "is_reverse True\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id VH01429:22:AACFJ5NHV:2:1608:28097:17679\n", - "VH01429:22:AACFJ5NHV:2:1608:28097:17679\t83\t#16\t83199827\t255\t100M1S\t#16\t83199827\t-100\tCATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACG\tarray('B', [34, 26, 12, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 26, 34, 34, 34, 12, 12, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 26, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 12, 34, 34, 34, 26, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 12])\t[('MD', '45C37G16'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 2), ('AS', 177)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 45C37G16\n", - "CIGAR string 100M1S\n", - "Reference seq: CATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTCTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAGTACTTTCCTGTAAAAC\n", - "Aligned seq: CATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACG\n", - "Qualities: array('B', [34, 26, 12, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 26, 34, 34, 34, 12, 12, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 26, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 12, 34, 34, 34, 26, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 12])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(0, 100), (4, 1)]\n", - "Aligned sequence before clipping (if needed):\n", - " CATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACG\n", - "Qualities before clipping:\n", - " array('B', [34, 26, 12, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 26, 34, 34, 34, 12, 12, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 26, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 12, 34, 34, 34, 26, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 12])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 100)]\n", - "Aligned sequence after clipping (if needed):\n", - " CATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAAC\n", - "Qualities after clipping:\n", - " array('B', [34, 26, 12, 34, 34, 34, 34, 26, 34, 34, 34, 26, 34, 34, 34, 34, 34, 26, 34, 34, 34, 12, 12, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 26, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 12, 34, 34, 34, 26, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['45', '37', '16']\n", - "[45, 83, 100]\n", - "Indicated reference seq:\n", - " catatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaaac\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " catatttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaaac\n", - "Fixed aligned seq:\n", - " CATATTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAAC\n", - "Finalized fixed aligned seq:\n", - " catatttccaactttattaatttttgcaagacttcggagggtgctGtgtggcgattaatattgctgagctgagcacagctgcaAtactttcctgtaaaac\n", - "Indicated qualities:\n", - " 34261234343434263434342634343434342634343412123434343426343434343434343434343434343434341226343434343434343434343434343426342612343434343434343434341234343434123434342612343434343434343434343412343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['G', 'A']\n", - "ref bases ['C', 'G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['G', 'A'], ref bases: ['C', 'G']\n", - "Getting info: G C 26 46\n", - "Getting info: A G 26 84\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 40C37G20\n", - "CIGAR tag 99M2S\n", - "is_reverse True\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id VH01429:22:AACFJ5NHV:2:1104:58090:46985\n", - "VH01429:22:AACFJ5NHV:2:1104:58090:46985\t83\t#16\t83199832\t255\t99M2S\t#16\t83195148\t-4783\tTTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGACCT\tarray('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 12, 26, 34, 34, 12, 34, 34, 34, 34, 34, 34, 12, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12])\t[('MD', '40C37G20'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 2), ('AS', 192), ('XS', '+')]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 40C37G20\n", - "CIGAR string 99M2S\n", - "Reference seq: TTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTCTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAGTACTTTCCTGTAAAACTGAC\n", - "Aligned seq: TTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGACCT\n", - "Qualities: array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 12, 26, 34, 34, 12, 34, 34, 34, 34, 34, 34, 12, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(0, 99), (4, 2)]\n", - "Aligned sequence before clipping (if needed):\n", - " TTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGACCT\n", - "Qualities before clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 12, 26, 34, 34, 12, 34, 34, 34, 34, 34, 34, 12, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 99)]\n", - "Aligned sequence after clipping (if needed):\n", - " TTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGAC\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 12, 26, 34, 34, 12, 34, 34, 34, 34, 34, 34, 12, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['40', '37', '20']\n", - "[40, 78, 99]\n", - "Indicated reference seq:\n", - " ttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaaactgac\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " ttccaactttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaaactgac\n", - "Fixed aligned seq:\n", - " TTCCAACTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGAC\n", - "Finalized fixed aligned seq:\n", - " ttccaactttattaatttttgcaagacttcggagggtgctGtgtggcgattaatattgctgagctgagcacagctgcaAtactttcctgtaaaactgac\n", - "Indicated qualities:\n", - " 343434343434343434263412263434123434343434341234342634343434343434343434343434343434343434343434342634343434343434263434343434343434343434262634343434343434342626123434343434343434343434343434343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['G', 'A']\n", - "ref bases ['C', 'G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['G', 'A'], ref bases: ['C', 'G']\n", - "Getting info: G C 34 41\n", - "Getting info: A G 34 79\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 33C37G19C9\n", - "CIGAR tag 101M\n", - "is_reverse True\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id VH01429:22:AACFJ5NHV:1:1109:44703:39053\n", - "VH01429:22:AACFJ5NHV:1:1109:44703:39053\t83\t#16\t83199839\t255\t101M\t#16\t83199777\t-163\tTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGATTAAAGGAGA\tarray('B', [34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12])\t[('MD', '33C37G19C9'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 3), ('AS', 191)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 33C37G19C9\n", - "CIGAR string 101M\n", - "Reference seq: TTTATTAATTTTTGCAAGACTTCGGAGGGTGCTCTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAGTACTTTCCTGTAAAACTGACTAAAGGAGA\n", - "Aligned seq: TTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGATTAAAGGAGA\n", - "Qualities: array('B', [34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(0, 101)]\n", - "Aligned sequence before clipping (if needed):\n", - " TTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGATTAAAGGAGA\n", - "Qualities before clipping:\n", - " array('B', [34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 101)]\n", - "Aligned sequence after clipping (if needed):\n", - " TTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGATTAAAGGAGA\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['33', '37', '19', '9']\n", - "[33, 71, 91, 101]\n", - "Indicated reference seq:\n", - " tttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaaactgaCtaaaggaga\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " tttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaaactgaCtaaaggaga\n", - "Fixed aligned seq:\n", - " TTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGATTAAAGGAGA\n", - "Finalized fixed aligned seq:\n", - " tttattaatttttgcaagacttcggagggtgctGtgtggcgattaatattgctgagctgagcacagctgcaAtactttcctgtaaaactgaTtaaaggaga\n", - "Indicated qualities:\n", - " 3434343426343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343412343434343434343434343412\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['G', 'A', 'T']\n", - "ref bases ['C', 'G', 'C']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['G', 'A', 'T'], ref bases: ['C', 'G', 'C']\n", - "Getting info: G C 34 34\n", - "Getting info: A G 34 72\n", - "Getting info: T C 34 92\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 33C37G29\n", - "CIGAR tag 101M\n", - "is_reverse True\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id VH01429:22:AACFJ5NHV:1:2414:26942:20235\n", - "VH01429:22:AACFJ5NHV:1:2414:26942:20235\t83\t#16\t83199839\t255\t101M\t#16\t83199825\t-115\tTTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGACTAAAGGAGA\tarray('B', [34, 34, 34, 34, 26, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 26, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 26])\t[('MD', '33C37G29'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 2), ('AS', 191)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 33C37G29\n", - "CIGAR string 101M\n", - "Reference seq: TTTATTAATTTTTGCAAGACTTCGGAGGGTGCTCTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAGTACTTTCCTGTAAAACTGACTAAAGGAGA\n", - "Aligned seq: TTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGACTAAAGGAGA\n", - "Qualities: array('B', [34, 34, 34, 34, 26, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 26, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 26])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(0, 101)]\n", - "Aligned sequence before clipping (if needed):\n", - " TTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGACTAAAGGAGA\n", - "Qualities before clipping:\n", - " array('B', [34, 34, 34, 34, 26, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 26, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 26])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 101)]\n", - "Aligned sequence after clipping (if needed):\n", - " TTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGACTAAAGGAGA\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 26, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 26, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 34, 34, 34, 26])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['33', '37', '29']\n", - "[33, 71, 101]\n", - "Indicated reference seq:\n", - " tttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaaactgactaaaggaga\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " tttattaatttttgcaagacttcggagggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaaactgactaaaggaga\n", - "Fixed aligned seq:\n", - " TTTATTAATTTTTGCAAGACTTCGGAGGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGACTAAAGGAGA\n", - "Finalized fixed aligned seq:\n", - " tttattaatttttgcaagacttcggagggtgctGtgtggcgattaatattgctgagctgagcacagctgcaAtactttcctgtaaaactgactaaaggaga\n", - "Indicated qualities:\n", - " 3434343426343426263434343434343434343434343426343434343434343412343434343434263412343434343434343434343434343434342634341234343434343434343434342626343434342634343434342634343434343434343434341234343426\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['G', 'A']\n", - "ref bases ['C', 'G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['G', 'A'], ref bases: ['C', 'G']\n", - "Getting info: G C 34 34\n", - "Getting info: A G 34 72\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 6C37G53\n", - "CIGAR tag 98M2S\n", - "is_reverse True\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id VH01429:22:AACFJ5NHV:2:1602:67558:13893\n", - "VH01429:22:AACFJ5NHV:2:1602:67558:13893\t83\t#16\t83199866\t255\t98M2S\t#16\t83195207\t-4757\tGGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGACTAAAGGAGAAGTTGGTGTCTTCCTCATACAAGAGA\tarray('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26])\t[('MD', '6C37G53'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 2), ('AS', 191), ('XS', '+')]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 6C37G53\n", - "CIGAR string 98M2S\n", - "Reference seq: GGTGCTCTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAGTACTTTCCTGTAAAACTGACTAAAGGAGAAGTTGGTGTCTTCCTCATACAAGA\n", - "Aligned seq: GGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGACTAAAGGAGAAGTTGGTGTCTTCCTCATACAAGAGA\n", - "Qualities: array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(0, 98), (4, 2)]\n", - "Aligned sequence before clipping (if needed):\n", - " GGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGACTAAAGGAGAAGTTGGTGTCTTCCTCATACAAGAGA\n", - "Qualities before clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 98)]\n", - "Aligned sequence after clipping (if needed):\n", - " GGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGACTAAAGGAGAAGTTGGTGTCTTCCTCATACAAGA\n", - "Qualities after clipping:\n", - " array('B', [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['6', '37', '53']\n", - "[6, 44, 98]\n", - "Indicated reference seq:\n", - " ggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaaactgactaaaggagaagttggtgtcttcctcatacaaga\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " ggtgctCtgtggcgattaatattgctgagctgagcacagctgcaGtactttcctgtaaaactgactaaaggagaagttggtgtcttcctcatacaaga\n", - "Fixed aligned seq:\n", - " GGTGCTGTGTGGCGATTAATATTGCTGAGCTGAGCACAGCTGCAATACTTTCCTGTAAAACTGACTAAAGGAGAAGTTGGTGTCTTCCTCATACAAGA\n", - "Finalized fixed aligned seq:\n", - " ggtgctGtgtggcgattaatattgctgagctgagcacagctgcaAtactttcctgtaaaactgactaaaggagaagttggtgtcttcctcatacaaga\n", - "Indicated qualities:\n", - " 3434343434343434343434343434343434343426343434343434343434343434343434343434343434343434343434343434263434343434343434343434343434343434343434343434343434343434343434343434343434343434343434343434\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['G', 'A']\n", - "ref bases ['C', 'G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['G', 'A'], ref bases: ['C', 'G']\n", - "Getting info: G C 34 7\n", - "Getting info: A G 34 45\n", - "chr17:015, total reads: 16, counts_df: chr17\n", - "edited 15\n", - "no_edits 1\n", - "chr17:004, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:011, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:003, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:009, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:001, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:006, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:012, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:002, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:008, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:014, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:007, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:013, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "Reads processed:\t16\n", - "Time to process reads in min:\t0.02411\n", - "Summary:\t chr17\n", - "edited 15\n", - "no_edits 1\n", - "\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Calculating coverage at edited sites, minimum read quality is 0...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "\tsplit chr17_000_0_5203591, 0/16...\n", - "\tsplit chr17_010_52035910_57239501, 10/16...\n", - "Done grouping! Concatenating ...\n", - "Done concatenating!\n", - "edit_info_grouped_per_contig_combined dict_keys(['chr17_000_0_5203591', 'chr17_001_5203591_10407182', 'chr17_002_10407182_15610773', 'chr17_003_15610773_20814364', 'chr17_004_20814364_26017955', 'chr17_005_26017955_31221546', 'chr17_006_31221546_36425137', 'chr17_007_36425137_41628728', 'chr17_008_41628728_46832319', 'chr17_009_46832319_52035910', 'chr17_010_52035910_57239501', 'chr17_011_57239501_62443092', 'chr17_012_62443092_67646683', 'chr17_013_67646683_72850274', 'chr17_014_72850274_78053865', 'chr17_015_78053865_83257456'])\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "100%|██████████| 16/16 [00:01<00:00, 11.96it/s]\n", - "100%|██████████| 16/16 [00:01<00:00, 11.99it/s]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Concatenating results...\n", - "Done concatenating.\n", - "Total time to calculate coverage: 0.024 minutes\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Filtering and calculating site-level statistics\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Loading edit information...\n", - "Filtering..\n", - "~~~~~~~~~~~~~~~~~~~~~~~\n", - "Filtering edited sites\n", - "~~~~~~~~~~~~~~~~~~~~~~~\n", - "Minimum distance from end = 0, Minimum base-calling quality = 0\n", - "Deduplicating....\n", - "\tNumber of edits before filtering:\n", - "\t32\n", - "\tNumber of edits after filtering:\n", - "\t32\n", - "\tNumber of edits after deduplicating:\n", - "\t24\n", - "\tNumber of unique edit sites:\n", - "\t10\n", - "Writing sites...\n", - "\n", - "Adding strand-specific conversion...\n", - "\n", - "10 sites being converted to SAILOR format...\n", - "0 rows had coverage of 0 or more edits than coverage... filtering these out, but look into them...\n", - "2 final deduplicated SAILOR-formatted sites\n", - "Annotating sites with GTF information from /tscc/projects/ps-yeolab3/ekofman/sailor2//annotations/hg38_gencode.v35.annotation.genes.bed...\n", - "Current memory usage 21.544627MB; Peak: 22.65451MB\n", - "Time elapsed: 3.80s\n", - "++++++\n", - "Done!\n", - "++++++\n", - "tax1bp3_chr17_3665556_read_test\n", - "Removing old files...\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "rm: cannot remove 'tests/strandedness_tests/tax1bp3_chr17_3665556_read_test/*': No such file or directory\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Running tests...\n", - "Assuming 16 cores available for multiprocessing. Set this to the number of available cores for optimal execution.\n", - "Arguments:\n", - "\tBAM filepath:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/bams/tax1bp3_chr17_3665556_read.bam\n", - "\tAnnotation bedfile filepath:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//annotations/hg38_gencode.v35.annotation.genes.bed\n", - "\tOutput folder:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/tax1bp3_chr17_3665556_read_test\n", - "\tBarcode whitelist:\tNone\n", - "\tStrandedness:\t2\n", - "\tBarcode Tag:\tNone\n", - "\tPaired End:\tTrue\n", - "\tCoverage only:\tFalse\n", - "\tFiltering only:\tFalse\n", - "\tAnnotation only:\tFalse\n", - "\tSailor outputs:\tTrue\n", - "\tMinimum base quality:\t0\n", - "\tMinimum read quality:\t0\n", - "\tMinimum distance from end:\t0\n", - "\tmax_edits_per_read:\tNone\n", - "\tContigs:\tchr17\n", - "\tNumber of intervals:\t16\n", - "\tCores:\t16\n", - "\tVerbose:\tTrue\n", - "\tSkip coverage?:\tFalse\n", - "\n", - ":::: :::: ::: ::::::::: ::::::::::: :::: ::: :::::::::: \n", - "+:+:+: :+:+:+ :+: :+: :+: :+: :+: :+:+: :+: :+: \n", - "+:+ +:+:+ +:+ +:+ +:+ +:+ +:+ +:+ :+:+:+ +:+ +:+ \n", - "+#+ +:+ +#+ +#++:++#++: +#++:++#: +#+ +#+ +:+ +#+ +#++:++# \n", - "+#+ +#+ +#+ +#+ +#+ +#+ +#+ +#+ +#+#+# +#+ \n", - "#+# #+# #+# #+# #+# #+# #+# #+# #+#+# #+# \n", - "### ### ### ### ### ### ########### ### #### ########## \n", - "==================================================================\n", - "Multi-core Algorithm for Rapid Identification of Nucleotide Edits\n", - "==================================================================\n", - "~~~~~~~~~~~~~~~~~~\n", - "Identifying edits\n", - "~~~~~~~~~~~~~~~~~~\n", - "Each contig is being split into 16 subsets...\n", - "contig_lengths_dict:{'chr1': 248956422, 'chr2': 242193529, 'chr3': 198295559, 'chr4': 190214555, 'chr5': 181538259, 'chr6': 170805979, 'chr7': 159345973, 'chr8': 145138636, 'chr9': 138394717, 'chr10': 133797422, 'chr11': 135086622, 'chr12': 133275309, 'chr13': 114364328, 'chr14': 107043718, 'chr15': 101991189, 'chr16': 90338345, 'chr17': 83257441, 'chr18': 80373285, 'chr19': 58617616, 'chr20': 64444167, 'chr21': 46709983, 'chr22': 50818468, 'chrX': 156040895, 'chrY': 57227415, 'chrM': 16569, 'chr1_KI270706v1_random': 175055, 'chr1_KI270707v1_random': 32032, 'chr1_KI270708v1_random': 127682, 'chr1_KI270709v1_random': 66860, 'chr1_KI270710v1_random': 40176, 'chr1_KI270711v1_random': 42210, 'chr1_KI270712v1_random': 176043, 'chr1_KI270713v1_random': 40745, 'chr1_KI270714v1_random': 41717, 'chr2_KI270715v1_random': 161471, 'chr2_KI270716v1_random': 153799, 'chr3_GL000221v1_random': 155397, 'chr4_GL000008v2_random': 209709, 'chr5_GL000208v1_random': 92689, 'chr9_KI270717v1_random': 40062, 'chr9_KI270718v1_random': 38054, 'chr9_KI270719v1_random': 176845, 'chr9_KI270720v1_random': 39050, 'chr11_KI270721v1_random': 100316, 'chr14_GL000009v2_random': 201709, 'chr14_GL000225v1_random': 211173, 'chr14_KI270722v1_random': 194050, 'chr14_GL000194v1_random': 191469, 'chr14_KI270723v1_random': 38115, 'chr14_KI270724v1_random': 39555, 'chr14_KI270725v1_random': 172810, 'chr14_KI270726v1_random': 43739, 'chr15_KI270727v1_random': 448248, 'chr16_KI270728v1_random': 1872759, 'chr17_GL000205v2_random': 185591, 'chr17_KI270729v1_random': 280839, 'chr17_KI270730v1_random': 112551, 'chr22_KI270731v1_random': 150754, 'chr22_KI270732v1_random': 41543, 'chr22_KI270733v1_random': 179772, 'chr22_KI270734v1_random': 165050, 'chr22_KI270735v1_random': 42811, 'chr22_KI270736v1_random': 181920, 'chr22_KI270737v1_random': 103838, 'chr22_KI270738v1_random': 99375, 'chr22_KI270739v1_random': 73985, 'chrY_KI270740v1_random': 37240, 'chrUn_KI270302v1': 2274, 'chrUn_KI270304v1': 2165, 'chrUn_KI270303v1': 1942, 'chrUn_KI270305v1': 1472, 'chrUn_KI270322v1': 21476, 'chrUn_KI270320v1': 4416, 'chrUn_KI270310v1': 1201, 'chrUn_KI270316v1': 1444, 'chrUn_KI270315v1': 2276, 'chrUn_KI270312v1': 998, 'chrUn_KI270311v1': 12399, 'chrUn_KI270317v1': 37690, 'chrUn_KI270412v1': 1179, 'chrUn_KI270411v1': 2646, 'chrUn_KI270414v1': 2489, 'chrUn_KI270419v1': 1029, 'chrUn_KI270418v1': 2145, 'chrUn_KI270420v1': 2321, 'chrUn_KI270424v1': 2140, 'chrUn_KI270417v1': 2043, 'chrUn_KI270422v1': 1445, 'chrUn_KI270423v1': 981, 'chrUn_KI270425v1': 1884, 'chrUn_KI270429v1': 1361, 'chrUn_KI270442v1': 392061, 'chrUn_KI270466v1': 1233, 'chrUn_KI270465v1': 1774, 'chrUn_KI270467v1': 3920, 'chrUn_KI270435v1': 92983, 'chrUn_KI270438v1': 112505, 'chrUn_KI270468v1': 4055, 'chrUn_KI270510v1': 2415, 'chrUn_KI270509v1': 2318, 'chrUn_KI270518v1': 2186, 'chrUn_KI270508v1': 1951, 'chrUn_KI270516v1': 1300, 'chrUn_KI270512v1': 22689, 'chrUn_KI270519v1': 138126, 'chrUn_KI270522v1': 5674, 'chrUn_KI270511v1': 8127, 'chrUn_KI270515v1': 6361, 'chrUn_KI270507v1': 5353, 'chrUn_KI270517v1': 3253, 'chrUn_KI270529v1': 1899, 'chrUn_KI270528v1': 2983, 'chrUn_KI270530v1': 2168, 'chrUn_KI270539v1': 993, 'chrUn_KI270538v1': 91309, 'chrUn_KI270544v1': 1202, 'chrUn_KI270548v1': 1599, 'chrUn_KI270583v1': 1400, 'chrUn_KI270587v1': 2969, 'chrUn_KI270580v1': 1553, 'chrUn_KI270581v1': 7046, 'chrUn_KI270579v1': 31033, 'chrUn_KI270589v1': 44474, 'chrUn_KI270590v1': 4685, 'chrUn_KI270584v1': 4513, 'chrUn_KI270582v1': 6504, 'chrUn_KI270588v1': 6158, 'chrUn_KI270593v1': 3041, 'chrUn_KI270591v1': 5796, 'chrUn_KI270330v1': 1652, 'chrUn_KI270329v1': 1040, 'chrUn_KI270334v1': 1368, 'chrUn_KI270333v1': 2699, 'chrUn_KI270335v1': 1048, 'chrUn_KI270338v1': 1428, 'chrUn_KI270340v1': 1428, 'chrUn_KI270336v1': 1026, 'chrUn_KI270337v1': 1121, 'chrUn_KI270363v1': 1803, 'chrUn_KI270364v1': 2855, 'chrUn_KI270362v1': 3530, 'chrUn_KI270366v1': 8320, 'chrUn_KI270378v1': 1048, 'chrUn_KI270379v1': 1045, 'chrUn_KI270389v1': 1298, 'chrUn_KI270390v1': 2387, 'chrUn_KI270387v1': 1537, 'chrUn_KI270395v1': 1143, 'chrUn_KI270396v1': 1880, 'chrUn_KI270388v1': 1216, 'chrUn_KI270394v1': 970, 'chrUn_KI270386v1': 1788, 'chrUn_KI270391v1': 1484, 'chrUn_KI270383v1': 1750, 'chrUn_KI270393v1': 1308, 'chrUn_KI270384v1': 1658, 'chrUn_KI270392v1': 971, 'chrUn_KI270381v1': 1930, 'chrUn_KI270385v1': 990, 'chrUn_KI270382v1': 4215, 'chrUn_KI270376v1': 1136, 'chrUn_KI270374v1': 2656, 'chrUn_KI270372v1': 1650, 'chrUn_KI270373v1': 1451, 'chrUn_KI270375v1': 2378, 'chrUn_KI270371v1': 2805, 'chrUn_KI270448v1': 7992, 'chrUn_KI270521v1': 7642, 'chrUn_GL000195v1': 182896, 'chrUn_GL000219v1': 179198, 'chrUn_GL000220v1': 161802, 'chrUn_GL000224v1': 179693, 'chrUn_KI270741v1': 157432, 'chrUn_GL000226v1': 15008, 'chrUn_GL000213v1': 164239, 'chrUn_KI270743v1': 210658, 'chrUn_KI270744v1': 168472, 'chrUn_KI270745v1': 41891, 'chrUn_KI270746v1': 66486, 'chrUn_KI270747v1': 198735, 'chrUn_KI270748v1': 93321, 'chrUn_KI270749v1': 158759, 'chrUn_KI270750v1': 148850, 'chrUn_KI270751v1': 150742, 'chrUn_KI270752v1': 27745, 'chrUn_KI270753v1': 62944, 'chrUn_KI270754v1': 40191, 'chrUn_KI270755v1': 36723, 'chrUn_KI270756v1': 79590, 'chrUn_KI270757v1': 71251, 'chrUn_GL000214v1': 137718, 'chrUn_KI270742v1': 186739, 'chrUn_GL000216v2': 176608, 'chrUn_GL000218v1': 161147, 'chrEBV': 171823}\n", - "\tContig chr17\n", - "16 total jobs\n", - "chr17:001, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:004, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:010, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:007, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:002, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:005, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:011, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 2C1C6G3A1G4G47\n", - "CIGAR tag 28S70M\n", - "is_reverse True\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id VH01429:22:AACFJ5NHV:2:2414:21053:15521\n", - "VH01429:22:AACFJ5NHV:2:2414:21053:15521\t83\t#16\t3665539\t255\t28S70M\t#16\t3665452\t-157\tCACAATAAGAGCCTATTTTGCTTCCTTAAAGGTGTGAAGTAAATTAATCATAAAAAGAAAGAAGCCAAAGAGAAAGGTACCTGGGTTCAACTAAAGCA\tarray('B', [26, 34, 34, 12, 12, 12, 26, 34, 34, 12, 34, 34, 12, 12, 26, 26, 12, 34, 12, 34, 12, 34, 34, 34, 12, 34, 12, 34, 34, 26, 12, 26, 34, 12, 34, 12, 34, 12, 26, 34, 26, 12, 34, 12, 34, 12, 12, 12, 12, 12, 12, 34, 34, 34, 34, 12, 12, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 12])\t[('MD', '2C1C6G3A1G4G47'), ('PG', 'MarkDuplicates'), ('RG', 'ET_STAMPExpt_1-CTRL_S2'), ('NH', 1), ('HI', 1), ('NM', 6), ('AS', 151)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 2C1C6G3A1G4G47\n", - "CIGAR string 28S70M\n", - "Reference seq: AACGCGTGAAGGAAAATGATCAGAAAAAGAAAGAAGCCAAAGAGAAAGGTACCTGGGTTCAACTAAAGCA\n", - "Aligned seq: CACAATAAGAGCCTATTTTGCTTCCTTAAAGGTGTGAAGTAAATTAATCATAAAAAGAAAGAAGCCAAAGAGAAAGGTACCTGGGTTCAACTAAAGCA\n", - "Qualities: array('B', [26, 34, 34, 12, 12, 12, 26, 34, 34, 12, 34, 34, 12, 12, 26, 26, 12, 34, 12, 34, 12, 34, 34, 34, 12, 34, 12, 34, 34, 26, 12, 26, 34, 12, 34, 12, 34, 12, 26, 34, 26, 12, 34, 12, 34, 12, 12, 12, 12, 12, 12, 34, 34, 34, 34, 12, 12, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 12])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 28), (0, 70)]\n", - "Aligned sequence before clipping (if needed):\n", - " CACAATAAGAGCCTATTTTGCTTCCTTAAAGGTGTGAAGTAAATTAATCATAAAAAGAAAGAAGCCAAAGAGAAAGGTACCTGGGTTCAACTAAAGCA\n", - "Qualities before clipping:\n", - " array('B', [26, 34, 34, 12, 12, 12, 26, 34, 34, 12, 34, 34, 12, 12, 26, 26, 12, 34, 12, 34, 12, 34, 34, 34, 12, 34, 12, 34, 34, 26, 12, 26, 34, 12, 34, 12, 34, 12, 26, 34, 26, 12, 34, 12, 34, 12, 12, 12, 12, 12, 12, 34, 34, 34, 34, 12, 12, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 12])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 70)]\n", - "Aligned sequence after clipping (if needed):\n", - " AAGGTGTGAAGTAAATTAATCATAAAAAGAAAGAAGCCAAAGAGAAAGGTACCTGGGTTCAACTAAAGCA\n", - "Qualities after clipping:\n", - " array('B', [34, 26, 12, 26, 34, 12, 34, 12, 34, 12, 26, 34, 26, 12, 34, 12, 34, 12, 12, 12, 12, 12, 12, 34, 34, 34, 34, 12, 12, 34, 34, 34, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 26, 34, 34, 34, 34, 34, 34, 34, 12])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['2', '1', '6', '3', '1', '4', '47']\n", - "[2, 4, 11, 15, 17, 22, 70]\n", - "Indicated reference seq:\n", - " aaCgCgtgaagGaaaAtGatcaGaaaaagaaagaagccaaagagaaaggtacctgggttcaactaaagca\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " aaCgCgtgaagGaaaAtGatcaGaaaaagaaagaagccaaagagaaaggtacctgggttcaactaaagca\n", - "Fixed aligned seq:\n", - " AAGGTGTGAAGTAAATTAATCATAAAAAGAAAGAAGCCAAAGAGAAAGGTACCTGGGTTCAACTAAAGCA\n", - "Finalized fixed aligned seq:\n", - " aaGgTgtgaagTaaaTtAatcaTaaaaagaaagaagccaaagagaaaggtacctgggttcaactaaagca\n", - "Indicated qualities:\n", - " 34261226341234123412263426123412341212121212123434343412123434341234343434343434343434343434343434343434343434343434343426263434343434343412\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['G', 'T', 'T', 'T', 'A', 'T']\n", - "ref bases ['C', 'C', 'G', 'A', 'G', 'G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['G', 'T', 'T', 'T', 'A', 'T'], ref bases: ['C', 'C', 'G', 'A', 'G', 'G']\n", - "Getting info: G C 12 3\n", - "Getting info: T C 34 5\n", - "Getting info: T G 34 12\n", - "Getting info: T A 12 16\n", - "Getting info: A G 12 18\n", - "Getting info: T G 12 23\n", - "chr17:000, total reads: 1, counts_df: chr17\n", - "edited 1\n", - "chr17:009, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:003, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:006, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:013, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:014, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:012, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:008, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "chr17:015, total reads: 0, counts_df: Empty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "Reads processed:\t1\n", - "Time to process reads in min:\t0.02257\n", - "Summary:\tEmpty DataFrame\n", - "Columns: []\n", - "Index: []\n", - "\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Calculating coverage at edited sites, minimum read quality is 0...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "\tsplit chr17_000_0_5203591, 0/16...\n", - "\tsplit chr17_010_52035910_57239501, 10/16...\n", - "Done grouping! Concatenating ...\n", - "Done concatenating!\n", - "edit_info_grouped_per_contig_combined dict_keys(['chr17_000_0_5203591', 'chr17_001_5203591_10407182', 'chr17_002_10407182_15610773', 'chr17_003_15610773_20814364', 'chr17_004_20814364_26017955', 'chr17_005_26017955_31221546', 'chr17_006_31221546_36425137', 'chr17_007_36425137_41628728', 'chr17_008_41628728_46832319', 'chr17_009_46832319_52035910', 'chr17_010_52035910_57239501', 'chr17_011_57239501_62443092', 'chr17_012_62443092_67646683', 'chr17_013_67646683_72850274', 'chr17_014_72850274_78053865', 'chr17_015_78053865_83257456'])\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "100%|██████████| 16/16 [00:01<00:00, 12.81it/s]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/tax1bp3_chr17_3665556_read_test/split_bams/chr17/chr17_000_0_5203591.bam.sorted.bam\n", - " chr17:3665541~~~~~~~`\n", - "coverage_at_pos 1\n", - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/tax1bp3_chr17_3665556_read_test/split_bams/chr17/chr17_000_0_5203591.bam.sorted.bam\n", - " chr17:3665543~~~~~~~`\n", - "coverage_at_pos 1\n", - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/tax1bp3_chr17_3665556_read_test/split_bams/chr17/chr17_000_0_5203591.bam.sorted.bam\n", - " chr17:3665550~~~~~~~`\n", - "coverage_at_pos 1\n", - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/tax1bp3_chr17_3665556_read_test/split_bams/chr17/chr17_000_0_5203591.bam.sorted.bam\n", - " chr17:3665554~~~~~~~`\n", - "coverage_at_pos 1\n", - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/tax1bp3_chr17_3665556_read_test/split_bams/chr17/chr17_000_0_5203591.bam.sorted.bam\n", - " chr17:3665556~~~~~~~`\n", - "coverage_at_pos 1\n", - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/tax1bp3_chr17_3665556_read_test/split_bams/chr17/chr17_000_0_5203591.bam.sorted.bam\n", - " chr17:3665561~~~~~~~`\n", - "coverage_at_pos 1\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "100%|██████████| 16/16 [00:01<00:00, 12.41it/s]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Concatenating results...\n", - "Done concatenating.\n", - "Total time to calculate coverage: 0.023 minutes\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Filtering and calculating site-level statistics\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Loading edit information...\n", - "Filtering..\n", - "~~~~~~~~~~~~~~~~~~~~~~~\n", - "Filtering edited sites\n", - "~~~~~~~~~~~~~~~~~~~~~~~\n", - "Minimum distance from end = 0, Minimum base-calling quality = 0\n", - "Deduplicating....\n", - "\tNumber of edits before filtering:\n", - "\t6\n", - "\tNumber of edits after filtering:\n", - "\t6\n", - "\tNumber of edits after deduplicating:\n", - "\t6\n", - "\tNumber of unique edit sites:\n", - "\t6\n", - "Writing sites...\n", - "\n", - "Adding strand-specific conversion...\n", - "\n", - "6 sites being converted to SAILOR format...\n", - "0 rows had coverage of 0 or more edits than coverage... filtering these out, but look into them...\n", - "1 final deduplicated SAILOR-formatted sites\n", - "Annotating sites with GTF information from /tscc/projects/ps-yeolab3/ekofman/sailor2//annotations/hg38_gencode.v35.annotation.genes.bed...\n", - "Current memory usage 21.445789MB; Peak: 22.556501MB\n", - "Time elapsed: 3.69s\n", - "++++++\n", - "Done!\n", - "++++++\n", - "pair_test\n", - "Removing old files...\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "rm: cannot remove 'tests/strandedness_tests/pair_test/*': No such file or directory\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Running tests...\n", - "Assuming 1 cores available for multiprocessing. Set this to the number of available cores for optimal execution.\n", - "Arguments:\n", - "\tBAM filepath:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/bams/pair_example_18_49488551_49590000.sorted.bam\n", - "\tAnnotation bedfile filepath:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//annotations/cellranger-GRCh38-3.0.0.annotation.genes.bed\n", - "\tOutput folder:\t/tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/pair_test\n", - "\tBarcode whitelist:\tNone\n", - "\tStrandedness:\t2\n", - "\tBarcode Tag:\tNone\n", - "\tPaired End:\tTrue\n", - "\tCoverage only:\tFalse\n", - "\tFiltering only:\tFalse\n", - "\tAnnotation only:\tFalse\n", - "\tSailor outputs:\tTrue\n", - "\tMinimum base quality:\t0\n", - "\tMinimum read quality:\t0\n", - "\tMinimum distance from end:\t0\n", - "\tmax_edits_per_read:\tNone\n", - "\tContigs:\t18\n", - "\tNumber of intervals:\t1\n", - "\tCores:\t1\n", - "\tVerbose:\tTrue\n", - "\tSkip coverage?:\tFalse\n", - "\n", - ":::: :::: ::: ::::::::: ::::::::::: :::: ::: :::::::::: \n", - "+:+:+: :+:+:+ :+: :+: :+: :+: :+: :+:+: :+: :+: \n", - "+:+ +:+:+ +:+ +:+ +:+ +:+ +:+ +:+ :+:+:+ +:+ +:+ \n", - "+#+ +:+ +#+ +#++:++#++: +#++:++#: +#+ +#+ +:+ +#+ +#++:++# \n", - "+#+ +#+ +#+ +#+ +#+ +#+ +#+ +#+ +#+#+# +#+ \n", - "#+# #+# #+# #+# #+# #+# #+# #+# #+#+# #+# \n", - "### ### ### ### ### ### ########### ### #### ########## \n", - "==================================================================\n", - "Multi-core Algorithm for Rapid Identification of Nucleotide Edits\n", - "==================================================================\n", - "~~~~~~~~~~~~~~~~~~\n", - "Identifying edits\n", - "~~~~~~~~~~~~~~~~~~\n", - "Each contig is being split into 1 subsets...\n", - "contig_lengths_dict:{'1': 248956422, '10': 133797422, '11': 135086622, '12': 133275309, '13': 114364328, '14': 107043718, '15': 101991189, '16': 90338345, '17': 83257441, '18': 80373285, '19': 58617616, '2': 242193529, '20': 64444167, '21': 46709983, '22': 50818468, '3': 198295559, '4': 190214555, '5': 181538259, '6': 170805979, '7': 159345973, '8': 145138636, '9': 138394717, 'MT': 16569, 'X': 156040895, 'Y': 57227415, 'KI270728.1': 1872759, 'KI270727.1': 448248, 'KI270442.1': 392061, 'KI270729.1': 280839, 'GL000225.1': 211173, 'KI270743.1': 210658, 'GL000008.2': 209709, 'GL000009.2': 201709, 'KI270747.1': 198735, 'KI270722.1': 194050, 'GL000194.1': 191469, 'KI270742.1': 186739, 'GL000205.2': 185591, 'GL000195.1': 182896, 'KI270736.1': 181920, 'KI270733.1': 179772, 'GL000224.1': 179693, 'GL000219.1': 179198, 'KI270719.1': 176845, 'GL000216.2': 176608, 'KI270712.1': 176043, 'KI270706.1': 175055, 'KI270725.1': 172810, 'KI270744.1': 168472, 'KI270734.1': 165050, 'GL000213.1': 164239, 'GL000220.1': 161802, 'KI270715.1': 161471, 'GL000218.1': 161147, 'KI270749.1': 158759, 'KI270741.1': 157432, 'GL000221.1': 155397, 'KI270716.1': 153799, 'KI270731.1': 150754, 'KI270751.1': 150742, 'KI270750.1': 148850, 'KI270519.1': 138126, 'GL000214.1': 137718, 'KI270708.1': 127682, 'KI270730.1': 112551, 'KI270438.1': 112505, 'KI270737.1': 103838, 'KI270721.1': 100316, 'KI270738.1': 99375, 'KI270748.1': 93321, 'KI270435.1': 92983, 'GL000208.1': 92689, 'KI270538.1': 91309, 'KI270756.1': 79590, 'KI270739.1': 73985, 'KI270757.1': 71251, 'KI270709.1': 66860, 'KI270746.1': 66486, 'KI270753.1': 62944, 'KI270589.1': 44474, 'KI270726.1': 43739, 'KI270735.1': 42811, 'KI270711.1': 42210, 'KI270745.1': 41891, 'KI270714.1': 41717, 'KI270732.1': 41543, 'KI270713.1': 40745, 'KI270754.1': 40191, 'KI270710.1': 40176, 'KI270717.1': 40062, 'KI270724.1': 39555, 'KI270720.1': 39050, 'KI270723.1': 38115, 'KI270718.1': 38054, 'KI270317.1': 37690, 'KI270740.1': 37240, 'KI270755.1': 36723, 'KI270707.1': 32032, 'KI270579.1': 31033, 'KI270752.1': 27745, 'KI270512.1': 22689, 'KI270322.1': 21476, 'GL000226.1': 15008, 'KI270311.1': 12399, 'KI270366.1': 8320, 'KI270511.1': 8127, 'KI270448.1': 7992, 'KI270521.1': 7642, 'KI270581.1': 7046, 'KI270582.1': 6504, 'KI270515.1': 6361, 'KI270588.1': 6158, 'KI270591.1': 5796, 'KI270522.1': 5674, 'KI270507.1': 5353, 'KI270590.1': 4685, 'KI270584.1': 4513, 'KI270320.1': 4416, 'KI270382.1': 4215, 'KI270468.1': 4055, 'KI270467.1': 3920, 'KI270362.1': 3530, 'KI270517.1': 3253, 'KI270593.1': 3041, 'KI270528.1': 2983, 'KI270587.1': 2969, 'KI270364.1': 2855, 'KI270371.1': 2805, 'KI270333.1': 2699, 'KI270374.1': 2656, 'KI270411.1': 2646, 'KI270414.1': 2489, 'KI270510.1': 2415, 'KI270390.1': 2387, 'KI270375.1': 2378, 'KI270420.1': 2321, 'KI270509.1': 2318, 'KI270315.1': 2276, 'KI270302.1': 2274, 'KI270518.1': 2186, 'KI270530.1': 2168, 'KI270304.1': 2165, 'KI270418.1': 2145, 'KI270424.1': 2140, 'KI270417.1': 2043, 'KI270508.1': 1951, 'KI270303.1': 1942, 'KI270381.1': 1930, 'KI270529.1': 1899, 'KI270425.1': 1884, 'KI270396.1': 1880, 'KI270363.1': 1803, 'KI270386.1': 1788, 'KI270465.1': 1774, 'KI270383.1': 1750, 'KI270384.1': 1658, 'KI270330.1': 1652, 'KI270372.1': 1650, 'KI270548.1': 1599, 'KI270580.1': 1553, 'KI270387.1': 1537, 'KI270391.1': 1484, 'KI270305.1': 1472, 'KI270373.1': 1451, 'KI270422.1': 1445, 'KI270316.1': 1444, 'KI270340.1': 1428, 'KI270338.1': 1428, 'KI270583.1': 1400, 'KI270334.1': 1368, 'KI270429.1': 1361, 'KI270393.1': 1308, 'KI270516.1': 1300, 'KI270389.1': 1298, 'KI270466.1': 1233, 'KI270388.1': 1216, 'KI270544.1': 1202, 'KI270310.1': 1201, 'KI270412.1': 1179, 'KI270395.1': 1143, 'KI270376.1': 1136, 'KI270337.1': 1121, 'KI270335.1': 1048, 'KI270378.1': 1048, 'KI270379.1': 1045, 'KI270329.1': 1040, 'KI270419.1': 1029, 'KI270336.1': 1026, 'KI270312.1': 998, 'KI270539.1': 993, 'KI270385.1': 990, 'KI270423.1': 981, 'KI270392.1': 971, 'KI270394.1': 970}\n", - "\tContig 18\n", - "1 total jobs\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 56G32\n", - "CIGAR tag 1S32M86N53M673N4M\n", - "is_reverse False\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse True\n", - "read id A00953:751:HNTFTDRX2:1:1275:16071:3552\n", - "A00953:751:HNTFTDRX2:1:1275:16071:3552\t99\t#9\t49491414\t3\t1S32M86N53M673N4M\t#9\t49491414\t848\tTAACACGAAGATTGGAACCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACCTCA\tarray('B', [25, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 37, 37, 37, 37, 25, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 25, 25, 37, 37, 37, 37, 37, 37, 25, 37, 11, 37, 37, 37, 25, 37, 37, 37])\t[('NH', 2), ('HI', 1), ('AS', 180), ('nM', 2), ('MD', '56G32'), ('NM', 1)]\n", - "reverse_or_forward: -\n", - "----------------------------\n", - "MD tag: 56G32\n", - "CIGAR string 1S32M86N53M673N4M\n", - "Reference seq: AACACGAAGATTGGAACCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAGTGAATAGCGAACCATTTTCACAGATCACCTCA\n", - "Aligned seq: TAACACGAAGATTGGAACCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACCTCA\n", - "Qualities: array('B', [25, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 37, 37, 37, 37, 25, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 25, 25, 37, 37, 37, 37, 37, 37, 25, 37, 11, 37, 37, 37, 25, 37, 37, 37])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 1), (0, 32), (3, 86), (0, 53), (3, 673), (0, 4)]\n", - "Aligned sequence before clipping (if needed):\n", - " TAACACGAAGATTGGAACCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACCTCA\n", - "Qualities before clipping:\n", - " array('B', [25, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 37, 37, 37, 37, 25, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 25, 25, 37, 37, 37, 37, 37, 37, 25, 37, 11, 37, 37, 37, 25, 37, 37, 37])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 32), (3, 86), (0, 53), (3, 673), (0, 4)]\n", - "Aligned sequence after clipping (if needed):\n", - " AACACGAAGATTGGAACCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACCTCA\n", - "Qualities after clipping:\n", - " array('B', [37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 37, 37, 37, 37, 25, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 25, 25, 37, 37, 37, 37, 37, 37, 25, 37, 11, 37, 37, 37, 25, 37, 37, 37])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['56', '32']\n", - "[56, 89]\n", - "Indicated reference seq:\n", - " aacacgaagattggaacctcttgatttgcatgatttcgtggggttctccgggtcaaGtgaatagcgaaccattttcacagatcacctca\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " aacacgaagattggaacctcttgatttgcatgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatttcgtggggttctccgggtcaaGtgaatagcgaaccattttcacagatcacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctca\n", - "Fixed aligned seq:\n", - " AACACGAAGATTGGAACCTCTTGATTTGCATGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnCTCA\n", - "Finalized fixed aligned seq:\n", - " aacacgaagattggaacctcttgatttgcatgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatttcgtggggttctccgggtcaaAtgaatagcgaaccattttcacagatcacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctca\n", - "Indicated qualities:\n", - " 3737373737373737113737373737373725372537373737373737373737373737373725373737373737373737253737373737373737373737373737253737372537373737373737252537373737373725371137373725373737\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['A']\n", - "ref bases ['G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['A'], ref bases: ['G']\n", - "Getting info: A G 37 143\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 56G32\n", - "CIGAR tag 1S32M86N53M673N4M\n", - "is_reverse True\n", - "is_read1 False\n", - "is_read2 True\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id A00953:751:HNTFTDRX2:1:1275:16071:3552\n", - "A00953:751:HNTFTDRX2:1:1275:16071:3552\t147\t#9\t49491414\t3\t1S32M86N53M673N4M\t#9\t49491414\t-848\tTAACACGAAGATTGGAACCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACCTCA\tarray('B', [37, 37, 11, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 25, 37, 37, 25, 37, 25, 37, 37, 37, 37, 37, 25, 25, 37, 37, 37, 25, 11, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 37, 37, 37, 25, 37, 25, 37, 37, 37, 37, 11, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37])\t[('NH', 2), ('HI', 1), ('AS', 180), ('nM', 2), ('MD', '56G32'), ('NM', 1)]\n", - "reverse_or_forward: -\n", - "----------------------------\n", - "MD tag: 56G32\n", - "CIGAR string 1S32M86N53M673N4M\n", - "Reference seq: AACACGAAGATTGGAACCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAGTGAATAGCGAACCATTTTCACAGATCACCTCA\n", - "Aligned seq: TAACACGAAGATTGGAACCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACCTCA\n", - "Qualities: array('B', [37, 37, 11, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 25, 37, 37, 25, 37, 25, 37, 37, 37, 37, 37, 25, 25, 37, 37, 37, 25, 11, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 37, 37, 37, 25, 37, 25, 37, 37, 37, 37, 11, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 1), (0, 32), (3, 86), (0, 53), (3, 673), (0, 4)]\n", - "Aligned sequence before clipping (if needed):\n", - " TAACACGAAGATTGGAACCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACCTCA\n", - "Qualities before clipping:\n", - " array('B', [37, 37, 11, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 25, 37, 37, 25, 37, 25, 37, 37, 37, 37, 37, 25, 25, 37, 37, 37, 25, 11, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 37, 37, 37, 25, 37, 25, 37, 37, 37, 37, 11, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 32), (3, 86), (0, 53), (3, 673), (0, 4)]\n", - "Aligned sequence after clipping (if needed):\n", - " AACACGAAGATTGGAACCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACCTCA\n", - "Qualities after clipping:\n", - " array('B', [37, 11, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 25, 37, 37, 25, 37, 25, 37, 37, 37, 37, 37, 25, 25, 37, 37, 37, 25, 11, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 37, 37, 37, 25, 37, 25, 37, 37, 37, 37, 11, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['56', '32']\n", - "[56, 89]\n", - "Indicated reference seq:\n", - " aacacgaagattggaacctcttgatttgcatgatttcgtggggttctccgggtcaaGtgaatagcgaaccattttcacagatcacctca\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " aacacgaagattggaacctcttgatttgcatgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatttcgtggggttctccgggtcaaGtgaatagcgaaccattttcacagatcacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctca\n", - "Fixed aligned seq:\n", - " AACACGAAGATTGGAACCTCTTGATTTGCATGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnCTCA\n", - "Finalized fixed aligned seq:\n", - " aacacgaagattggaacctcttgatttgcatgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatttcgtggggttctccgggtcaaAtgaatagcgaaccattttcacagatcacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctca\n", - "Indicated qualities:\n", - " 3711373737373737373737253737372537372537253737373737252537373725113737372537373737373737371137373737373725372537373737113737373725373737373737373737373725373737373737373737373737\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['A']\n", - "ref bases ['G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['A'], ref bases: ['G']\n", - "Getting info: A G 37 143\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 40G59\n", - "CIGAR tag 1S16M86N53M690N31M\n", - "is_reverse False\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse True\n", - "read id A00953:751:HNTFTDRX2:2:1273:9652:13761\n", - "A00953:751:HNTFTDRX2:2:1273:9652:13761\t99\t#9\t49491430\t255\t1S16M86N53M690N31M\t#9\t49492336\t1006\tTCCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACCCCGGCTCCCAAAGTCAGGCCCTCCGCCACG\tarray('B', [11, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 25, 37, 37, 11, 25, 37, 37, 37, 37, 25, 25, 37, 25, 37, 37, 37, 25, 37, 25, 11, 37, 25, 37, 25, 25, 37, 37, 37, 37, 37, 11, 37, 37, 37, 11, 37, 11, 25, 11, 37, 37, 37, 11, 37, 11, 11, 11, 37, 37, 37, 11, 37, 37, 37, 11, 25, 37, 25, 25, 37, 25, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 25, 37, 11, 25, 37, 11, 37, 25, 25, 25, 37, 37, 37, 25])\t[('NH', 1), ('HI', 1), ('AS', 200), ('nM', 1), ('MD', '40G59'), ('NM', 1)]\n", - "reverse_or_forward: -\n", - "----------------------------\n", - "MD tag: 40G59\n", - "CIGAR string 1S16M86N53M690N31M\n", - "Reference seq: CCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAGTGAATAGCGAACCATTTTCACAGATCACCCCGGCTCCCAAAGTCAGGCCCTCCGCCACG\n", - "Aligned seq: TCCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACCCCGGCTCCCAAAGTCAGGCCCTCCGCCACG\n", - "Qualities: array('B', [11, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 25, 37, 37, 11, 25, 37, 37, 37, 37, 25, 25, 37, 25, 37, 37, 37, 25, 37, 25, 11, 37, 25, 37, 25, 25, 37, 37, 37, 37, 37, 11, 37, 37, 37, 11, 37, 11, 25, 11, 37, 37, 37, 11, 37, 11, 11, 11, 37, 37, 37, 11, 37, 37, 37, 11, 25, 37, 25, 25, 37, 25, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 25, 37, 11, 25, 37, 11, 37, 25, 25, 25, 37, 37, 37, 25])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(4, 1), (0, 16), (3, 86), (0, 53), (3, 690), (0, 31)]\n", - "Aligned sequence before clipping (if needed):\n", - " TCCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACCCCGGCTCCCAAAGTCAGGCCCTCCGCCACG\n", - "Qualities before clipping:\n", - " array('B', [11, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 25, 37, 37, 11, 25, 37, 37, 37, 37, 25, 25, 37, 25, 37, 37, 37, 25, 37, 25, 11, 37, 25, 37, 25, 25, 37, 37, 37, 37, 37, 11, 37, 37, 37, 11, 37, 11, 25, 11, 37, 37, 37, 11, 37, 11, 11, 11, 37, 37, 37, 11, 37, 37, 37, 11, 25, 37, 25, 25, 37, 25, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 25, 37, 11, 25, 37, 11, 37, 25, 25, 25, 37, 37, 37, 25])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 16), (3, 86), (0, 53), (3, 690), (0, 31)]\n", - "Aligned sequence after clipping (if needed):\n", - " CCTCTTGATTTGCATGATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACCCCGGCTCCCAAAGTCAGGCCCTCCGCCACG\n", - "Qualities after clipping:\n", - " array('B', [37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 25, 37, 37, 11, 25, 37, 37, 37, 37, 25, 25, 37, 25, 37, 37, 37, 25, 37, 25, 11, 37, 25, 37, 25, 25, 37, 37, 37, 37, 37, 11, 37, 37, 37, 11, 37, 11, 25, 11, 37, 37, 37, 11, 37, 11, 11, 11, 37, 37, 37, 11, 37, 37, 37, 11, 25, 37, 25, 25, 37, 25, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 25, 37, 11, 25, 37, 11, 37, 25, 25, 25, 37, 37, 37, 25])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['40', '59']\n", - "[40, 100]\n", - "Indicated reference seq:\n", - " cctcttgatttgcatgatttcgtggggttctccgggtcaaGtgaatagcgaaccattttcacagatcaccccggctcccaaagtcaggccctccgccacg\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " cctcttgatttgcatgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatttcgtggggttctccgggtcaaGtgaatagcgaaccattttcacagatcacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncccggctcccaaagtcaggccctccgccacg\n", - "Fixed aligned seq:\n", - " CCTCTTGATTTGCATGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnATTTCGTGGGGTTCTCCGGGTCAAATGAATAGCGAACCATTTTCACAGATCACnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnCCCGGCTCCCAAAGTCAGGCCCTCCGCCACG\n", - "Finalized fixed aligned seq:\n", - " cctcttgatttgcatgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatttcgtggggttctccgggtcaaAtgaatagcgaaccattttcacagatcacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncccggctcccaaagtcaggccctccgccacg\n", - "Indicated qualities:\n", - " 37373737253737373737372537371125373737372525372537373725372511372537252537373737371137373711371125113737371137111111373737113737371125372525372537373725373737373737371137372537112537113725252537373725\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['A']\n", - "ref bases ['G']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['A'], ref bases: ['G']\n", - "Getting info: A G 37 127\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 90C10\n", - "CIGAR tag 38M1943N63M\n", - "is_reverse False\n", - "is_read1 False\n", - "is_read2 True\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse True\n", - "read id A00953:751:HNTFTDRX2:2:2163:27172:16110\n", - "A00953:751:HNTFTDRX2:2:2163:27172:16110\t163\t#9\t49565461\t255\t38M1943N63M\t#9\t49565495\t2076\tTGACAGCTAAAACCTTTTTCATCATTCACGGATGGACGATGAGCGGTATCTTTGAAAACTGGCTGCACAAACTCGTGTCAGCCCTGCACATAAGAGAGAAA\tarray('B', [37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37])\t[('NH', 1), ('HI', 1), ('AS', 197), ('nM', 2), ('MD', '90C10'), ('NM', 1)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 90C10\n", - "CIGAR string 38M1943N63M\n", - "Reference seq: TGACAGCTAAAACCTTTTTCATCATTCACGGATGGACGATGAGCGGTATCTTTGAAAACTGGCTGCACAAACTCGTGTCAGCCCTGCACACAAGAGAGAAA\n", - "Aligned seq: TGACAGCTAAAACCTTTTTCATCATTCACGGATGGACGATGAGCGGTATCTTTGAAAACTGGCTGCACAAACTCGTGTCAGCCCTGCACATAAGAGAGAAA\n", - "Qualities: array('B', [37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(0, 38), (3, 1943), (0, 63)]\n", - "Aligned sequence before clipping (if needed):\n", - " TGACAGCTAAAACCTTTTTCATCATTCACGGATGGACGATGAGCGGTATCTTTGAAAACTGGCTGCACAAACTCGTGTCAGCCCTGCACATAAGAGAGAAA\n", - "Qualities before clipping:\n", - " array('B', [37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 38), (3, 1943), (0, 63)]\n", - "Aligned sequence after clipping (if needed):\n", - " TGACAGCTAAAACCTTTTTCATCATTCACGGATGGACGATGAGCGGTATCTTTGAAAACTGGCTGCACAAACTCGTGTCAGCCCTGCACATAAGAGAGAAA\n", - "Qualities after clipping:\n", - " array('B', [37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['90', '10']\n", - "[90, 101]\n", - "Indicated reference seq:\n", - " tgacagctaaaacctttttcatcattcacggatggacgatgagcggtatctttgaaaactggctgcacaaactcgtgtcagccctgcacaCaagagagaaa\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " tgacagctaaaacctttttcatcattcacggatggacg1943*natgagcggtatctttgaaaactggctgcacaaactcgtgtcagccctgcacaCaagagagaaa\n", - "Fixed aligned seq:\n", - " TGACAGCTAAAACCTTTTTCATCATTCACGGATGGACG1943*nATGAGCGGTATCTTTGAAAACTGGCTGCACAAACTCGTGTCAGCCCTGCACATAAGAGAGAAA\n", - "Finalized fixed aligned seq:\n", - " tgacagctaaaacctttttcatcattcacggatggacg1943*natgagcggtatctttgaaaactggctgcacaaactcgtgtcagccctgcacaTaagagagaaa\n", - "Indicated qualities:\n", - " 3737253737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737371137373737373737373737373737373737373737373737373737373737373737373737373737373737373737\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['T']\n", - "ref bases ['C']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['T'], ref bases: ['C']\n", - "Getting info: T C 37 2034\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 56C42\n", - "CIGAR tag 4M1943N95M1S\n", - "is_reverse True\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id A00953:751:HNTFTDRX2:2:2163:27172:16110\n", - "A00953:751:HNTFTDRX2:2:2163:27172:16110\t83\t#9\t49565495\t255\t4M1943N95M1S\t#9\t49565461\t-2076\tGACGATGAGCGGTATCTTTGAAAACTGGCTGCACAAACTCGTGTCAGCCCTGCACATAAGAGAGAAAGACGCCAATGTAGTTGTGGTTGACTGGCTCCCA\tarray('B', [37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37])\t[('NH', 1), ('HI', 1), ('AS', 197), ('nM', 2), ('MD', '56C42'), ('NM', 1)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 56C42\n", - "CIGAR string 4M1943N95M1S\n", - "Reference seq: GACGATGAGCGGTATCTTTGAAAACTGGCTGCACAAACTCGTGTCAGCCCTGCACACAAGAGAGAAAGACGCCAATGTAGTTGTGGTTGACTGGCTCCC\n", - "Aligned seq: GACGATGAGCGGTATCTTTGAAAACTGGCTGCACAAACTCGTGTCAGCCCTGCACATAAGAGAGAAAGACGCCAATGTAGTTGTGGTTGACTGGCTCCCA\n", - "Qualities: array('B', [37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(0, 4), (3, 1943), (0, 95), (4, 1)]\n", - "Aligned sequence before clipping (if needed):\n", - " GACGATGAGCGGTATCTTTGAAAACTGGCTGCACAAACTCGTGTCAGCCCTGCACATAAGAGAGAAAGACGCCAATGTAGTTGTGGTTGACTGGCTCCCA\n", - "Qualities before clipping:\n", - " array('B', [37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 4), (3, 1943), (0, 95)]\n", - "Aligned sequence after clipping (if needed):\n", - " GACGATGAGCGGTATCTTTGAAAACTGGCTGCACAAACTCGTGTCAGCCCTGCACATAAGAGAGAAAGACGCCAATGTAGTTGTGGTTGACTGGCTCCC\n", - "Qualities after clipping:\n", - " array('B', [37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['56', '42']\n", - "[56, 99]\n", - "Indicated reference seq:\n", - " gacgatgagcggtatctttgaaaactggctgcacaaactcgtgtcagccctgcacaCaagagagaaagacgccaatgtagttgtggttgactggctccc\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " gacg1943*natgagcggtatctttgaaaactggctgcacaaactcgtgtcagccctgcacaCaagagagaaagacgccaatgtagttgtggttgactggctccc\n", - "Fixed aligned seq:\n", - " GACG1943*nATGAGCGGTATCTTTGAAAACTGGCTGCACAAACTCGTGTCAGCCCTGCACATAAGAGAGAAAGACGCCAATGTAGTTGTGGTTGACTGGCTCCC\n", - "Finalized fixed aligned seq:\n", - " gacg1943*natgagcggtatctttgaaaactggctgcacaaactcgtgtcagccctgcacaTaagagagaaagacgccaatgtagttgtggttgactggctccc\n", - "Indicated qualities:\n", - " 373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737373737\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['T']\n", - "ref bases ['C']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['T'], ref bases: ['C']\n", - "Getting info: T C 37 2000\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "MD tag 13C85\n", - "CIGAR tag 99M1S\n", - "is_reverse True\n", - "is_read1 True\n", - "is_read2 False\n", - "is_paired True\n", - "is_proper_pair True\n", - "mate_is_reverse False\n", - "read id A00953:751:HNTFTDRX2:2:2111:15808:2284\n", - "A00953:751:HNTFTDRX2:2:2111:15808:2284\t83\t#9\t49567481\t255\t99M1S\t#9\t49565425\t-2155\tTCAGCCCTGCACATAAGAGAGAAAGACGCCAATGTAGTTGTGGTTGACTGGCTCCCCCTGGCCCACCAGCTTTACACGGATGCGGTCAATAATACCAGGA\tarray('B', [36, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 11, 25, 37, 25, 37, 37, 25, 25, 37, 25, 37, 37, 37, 37, 37, 11, 37, 11, 25, 37, 37, 37, 25, 37, 11, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 11, 37, 37, 37, 37, 25, 37, 37, 37, 37, 25, 37, 37, 37, 11, 37, 37, 37, 37, 25, 37, 37, 37, 25, 37, 25, 37, 11, 28, 11, 25])\t[('NH', 1), ('HI', 1), ('AS', 194), ('nM', 1), ('MD', '13C85'), ('ZQ', 'A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@I@@'), ('NM', 1)]\n", - "reverse_or_forward: +\n", - "----------------------------\n", - "MD tag: 13C85\n", - "CIGAR string 99M1S\n", - "Reference seq: TCAGCCCTGCACACAAGAGAGAAAGACGCCAATGTAGTTGTGGTTGACTGGCTCCCCCTGGCCCACCAGCTTTACACGGATGCGGTCAATAATACCAGG\n", - "Aligned seq: TCAGCCCTGCACATAAGAGAGAAAGACGCCAATGTAGTTGTGGTTGACTGGCTCCCCCTGGCCCACCAGCTTTACACGGATGCGGTCAATAATACCAGGA\n", - "Qualities: array('B', [36, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 11, 25, 37, 25, 37, 37, 25, 25, 37, 25, 37, 37, 37, 37, 37, 11, 37, 11, 25, 37, 37, 37, 25, 37, 11, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 11, 37, 37, 37, 37, 25, 37, 37, 37, 37, 25, 37, 37, 37, 11, 37, 37, 37, 37, 25, 37, 37, 37, 25, 37, 25, 37, 11, 28, 11, 25])\n", - "CIGAR tuples before clipping (if needed):\n", - " [(0, 99), (4, 1)]\n", - "Aligned sequence before clipping (if needed):\n", - " TCAGCCCTGCACATAAGAGAGAAAGACGCCAATGTAGTTGTGGTTGACTGGCTCCCCCTGGCCCACCAGCTTTACACGGATGCGGTCAATAATACCAGGA\n", - "Qualities before clipping:\n", - " array('B', [36, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 11, 25, 37, 25, 37, 37, 25, 25, 37, 25, 37, 37, 37, 37, 37, 11, 37, 11, 25, 37, 37, 37, 25, 37, 11, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 11, 37, 37, 37, 37, 25, 37, 37, 37, 37, 25, 37, 37, 37, 11, 37, 37, 37, 37, 25, 37, 37, 37, 25, 37, 25, 37, 11, 28, 11, 25])\n", - "Soft clipping quality scores ...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "CIGAR tuples after clipping (if needed):\n", - " [(0, 99)]\n", - "Aligned sequence after clipping (if needed):\n", - " TCAGCCCTGCACATAAGAGAGAAAGACGCCAATGTAGTTGTGGTTGACTGGCTCCCCCTGGCCCACCAGCTTTACACGGATGCGGTCAATAATACCAGG\n", - "Qualities after clipping:\n", - " array('B', [36, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 11, 25, 37, 25, 37, 37, 25, 25, 37, 25, 37, 37, 37, 37, 37, 11, 37, 11, 25, 37, 37, 37, 25, 37, 11, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 37, 37, 37, 11, 37, 37, 37, 37, 25, 37, 37, 37, 37, 25, 37, 37, 37, 11, 37, 37, 37, 37, 25, 37, 37, 37, 25, 37, 25, 37, 11, 28, 11])\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "['13', '85']\n", - "[13, 99]\n", - "Indicated reference seq:\n", - " tcagccctgcacaCaagagagaaagacgccaatgtagttgtggttgactggctccccctggcccaccagctttacacggatgcggtcaataataccagg\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Fixed reference seq:\n", - " tcagccctgcacaCaagagagaaagacgccaatgtagttgtggttgactggctccccctggcccaccagctttacacggatgcggtcaataataccagg\n", - "Fixed aligned seq:\n", - " TCAGCCCTGCACATAAGAGAGAAAGACGCCAATGTAGTTGTGGTTGACTGGCTCCCCCTGGCCCACCAGCTTTACACGGATGCGGTCAATAATACCAGG\n", - "Finalized fixed aligned seq:\n", - " tcagccctgcacaTaagagagaaagacgccaatgtagttgtggttgactggctccccctggcccaccagctttacacggatgcggtcaataataccagg\n", - "Indicated qualities:\n", - " 363737373737253737373711253725373725253725373737373711371125373737253711373737373725373737373737373737373737372537373737373737373711373737113737373725373737372537373711373737372537373725372537112811\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "alt bases ['T']\n", - "ref bases ['C']\n", - "Successfully ran get_edit_information_wrapper\n", - "alt bases: ['T'], ref bases: ['C']\n", - "Getting info: T C 37 14\n", - "18:000, total reads: 10, counts_df: 18\n", - "edited 6\n", - "no_edits 2\n", - "secondary 2\n", - "Reads processed:\t10\n", - "Time to process reads in min:\t0.03715\n", - "Summary:\t 18\n", - "edited 6\n", - "no_edits 2\n", - "secondary 2\n", - "\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Calculating coverage at edited sites, minimum read quality is 0...\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "\tsplit 18_000_0_80373285, 0/1...\n", - "Done grouping! Concatenating ...\n", - "Done concatenating!\n", - "edit_info_grouped_per_contig_combined dict_keys(['18_000_0_80373285'])\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "100%|██████████| 1/1 [00:02<00:00, 2.19s/it]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/pair_test/split_bams/18/18_000_0_80373285.bam.sorted.bam\n", - " 18:49491556~~~~~~~`\n", - "coverage_at_pos 2\n", - "~~~~~~\n", - "!!!!PAIRED END!!!!!\n", - "pos: /tscc/projects/ps-yeolab3/ekofman/sailor2//tests/strandedness_tests/pair_test/split_bams/18/18_000_0_80373285.bam.sorted.bam\n", - " 18:49567494~~~~~~~`\n", - "coverage_at_pos 2\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "100%|██████████| 1/1 [00:02<00:00, 2.01s/it]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Concatenating results...\n", - "Done concatenating.\n", - "Total time to calculate coverage: 0.034 minutes\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Filtering and calculating site-level statistics\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Loading edit information...\n", - "Filtering..\n", - "~~~~~~~~~~~~~~~~~~~~~~~\n", - "Filtering edited sites\n", - "~~~~~~~~~~~~~~~~~~~~~~~\n", - "Minimum distance from end = 0, Minimum base-calling quality = 0\n", - "Deduplicating....\n", - "\tNumber of edits before filtering:\n", - "\t5\n", - "\tNumber of edits after filtering:\n", - "\t5\n", - "\tNumber of edits after deduplicating:\n", - "\t4\n", - "\tNumber of unique edit sites:\n", - "\t2\n", - "Writing sites...\n", - "\n", - "Adding strand-specific conversion...\n", - "\n", - "2 sites being converted to SAILOR format...\n", - "0 rows had coverage of 0 or more edits than coverage... filtering these out, but look into them...\n", - "2 final deduplicated SAILOR-formatted sites\n", - "Annotating sites with GTF information from /tscc/projects/ps-yeolab3/ekofman/sailor2//annotations/cellranger-GRCh38-3.0.0.annotation.genes.bed...\n", - "Current memory usage 21.445743MB; Peak: 22.555779MB\n", - "Time elapsed: 5.35s\n", + "Current memory usage 21.673684MB; Peak: 22.78224MB\n", + "Time elapsed: 4.74s\n", + "-------------------------------\n", + "Deleting intermediate files...\n", + "-------------------------------\n", "++++++\n", "Done!\n", "++++++\n" @@ -2640,7 +217,7 @@ "export MARINE=/tscc/projects/ps-yeolab3/ekofman/sailor2/\n", "export mypython=/tscc/nfs/home/ekofman/miniconda3/envs/marine_environment/bin/python\n", "\n", - "for t in \"unstranded_pair_test\" \"F1R2_pair_test-single_end_mode\" \"F1R2_pair_test\" \"F2R1_end_second_in_pair_test\" \"same_pos_dif_reads_test\" \"tax1bp3_chr17_3665556_read_test\" \"pair_test\"\n", + "for t in \"unstranded_pair_test\" # \"F1R2_pair_test-single_end_mode\" \"F1R2_pair_test\" \"F2R1_end_second_in_pair_test\" \"same_pos_dif_reads_test\" \"tax1bp3_chr17_3665556_read_test\" \"pair_test\"\n", "\n", "do\n", " echo $t\n", diff --git a/tests/strandedness_tests/scripts/unstranded_pair_test.sh b/tests/strandedness_tests/scripts/unstranded_pair_test.sh index 0bb2d2b..151ded4 100644 --- a/tests/strandedness_tests/scripts/unstranded_pair_test.sh +++ b/tests/strandedness_tests/scripts/unstranded_pair_test.sh @@ -15,5 +15,5 @@ $MARINE/tests/strandedness_tests/unstranded_pair_test \ 1 \ --paired_end \ --strandedness 0 \ ---sailor \ +--sailor --bedgraphs "CT" \ --num_intervals_per_contig 1 \ No newline at end of file diff --git a/tests/strandedness_tests/unstranded_pair_test/final_filtered_site_info.tsv b/tests/strandedness_tests/unstranded_pair_test/final_filtered_site_info.tsv index bcfac7e..07c506c 100644 --- a/tests/strandedness_tests/unstranded_pair_test/final_filtered_site_info.tsv +++ b/tests/strandedness_tests/unstranded_pair_test/final_filtered_site_info.tsv @@ -1,15 +1,15 @@ site_id barcode contig position ref alt strand count coverage conversion strand_conversion +no_barcode_Citrine.dna_414_G_C_+ no_barcode Citrine.dna 414 G C + 1 18 G>C G>C no_barcode_Citrine.dna_437_A_G_+ no_barcode Citrine.dna 437 A G + 1 22 A>G A>G -no_barcode_Citrine.dna_431_A_G_+ no_barcode Citrine.dna 431 A G + 1 22 A>G A>G -no_barcode_Citrine.dna_454_T_G_+ no_barcode Citrine.dna 454 T G + 1 14 T>G T>G -no_barcode_Citrine.dna_439_A_G_+ no_barcode Citrine.dna 439 A G + 1 22 A>G A>G no_barcode_Citrine.dna_435_C_T_+ no_barcode Citrine.dna 435 C T + 22 22 C>T C>T -no_barcode_Citrine.dna_428_A_G_+ no_barcode Citrine.dna 428 A G + 1 20 A>G A>G -no_barcode_Citrine.dna_414_G_C_+ no_barcode Citrine.dna 414 G C + 1 18 G>C G>C -no_barcode_Citrine.dna_21_G_A_+ no_barcode Citrine.dna 21 G A + 2 2 G>A G>A -no_barcode_Citrine.dna_441_C_A_+ no_barcode Citrine.dna 441 C A + 1 22 C>A C>A -no_barcode_Citrine.dna_438_C_A_+ no_barcode Citrine.dna 438 C A + 1 22 C>A C>A no_barcode_Citrine.dna_149_C_G_+ no_barcode Citrine.dna 149 C G + 1 2 C>G C>G +no_barcode_Citrine.dna_441_C_A_+ no_barcode Citrine.dna 441 C A + 1 22 C>A C>A no_barcode_Citrine.dna_411_C_A_+ no_barcode Citrine.dna 411 C A + 1 18 C>A C>A +no_barcode_Citrine.dna_431_A_G_+ no_barcode Citrine.dna 431 A G + 1 22 A>G A>G +no_barcode_Citrine.dna_21_G_A_+ no_barcode Citrine.dna 21 G A + 2 2 G>A G>A no_barcode_Citrine.dna_432_C_T_+ no_barcode Citrine.dna 432 C T + 1 22 C>T C>T +no_barcode_Citrine.dna_439_A_G_+ no_barcode Citrine.dna 439 A G + 1 22 A>G A>G +no_barcode_Citrine.dna_438_C_A_+ no_barcode Citrine.dna 438 C A + 1 22 C>A C>A no_barcode_Citrine.dna_430_T_G_+ no_barcode Citrine.dna 430 T G + 2 22 T>G T>G +no_barcode_Citrine.dna_454_T_G_+ no_barcode Citrine.dna 454 T G + 1 14 T>G T>G +no_barcode_Citrine.dna_428_A_G_+ no_barcode Citrine.dna 428 A G + 1 20 A>G A>G