From c4b3d0c7e19396b5058c6298f443441a8e4b93a9 Mon Sep 17 00:00:00 2001 From: Eric Kofman Date: Mon, 9 Dec 2024 21:22:16 -0800 Subject: [PATCH] test fix --- .../depth_commands_source_cells.txt | 2 - src/utils.py | 4 +- tests/integration_tests.ipynb | 42 +++++++++---------- .../scripts/long_read_sc_test.sh | 2 +- 4 files changed, 23 insertions(+), 27 deletions(-) delete mode 100644 examples/sc_subset_CT/depth_commands_source_cells.txt diff --git a/examples/sc_subset_CT/depth_commands_source_cells.txt b/examples/sc_subset_CT/depth_commands_source_cells.txt deleted file mode 100644 index 6531b69..0000000 --- a/examples/sc_subset_CT/depth_commands_source_cells.txt +++ /dev/null @@ -1,2 +0,0 @@ -echo 'concatenating bed file...';for file in /tscc/projects/ps-yeolab3/ekofman/sailor2/examples/sc_subset_CT/edit_info/*edit_info.tsv; do awk 'NR > 1 {print $2, $4-1, $4}' OFS=' ' "$file"; done | sort -k1,1 -k2,2n -u > /tscc/projects/ps-yeolab3/ekofman/sailor2/examples/sc_subset_CT/combined_source_cells.bed; - diff --git a/src/utils.py b/src/utils.py index 0b5ac5d..fdb9cd1 100644 --- a/src/utils.py +++ b/src/utils.py @@ -1109,10 +1109,10 @@ def delete_intermediate_files(output_folder): 'combined_source_cells_split_by_suffix', 'matrix_outputs', 'all_edit_info.tsv', - 'concat_command.sh', 'depth_commands_source_cells.sh', 'combined.bed', 'merge_command.sh', + 'concat_command.sh', 'depth_commands_source_cells.sh', 'depth_commands_source_cells.txt', 'combined.bed', 'merge_command.sh', 'final_edit_info_no_coverage.tsv', 'final_edit_info_no_coverage_sorted.tsv', 'depths_source_cells.txt', 'depth_modified.tsv', 'final_edit_info.tsv', 'final_filtered_edit_info.tsv', - 'combined_all_cells.bed', 'depth_commands_all_cells.sh', 'depths_all_cells.txt', 'combined_source_cells.bed' + 'combined_all_cells.bed', 'depth_commands_all_cells.sh', 'depth_commands_all_cells.txt', 'depths_all_cells.txt', 'combined_source_cells.bed' ] for object in to_delete: object_path = '{}/{}'.format(output_folder, object) diff --git a/tests/integration_tests.ipynb b/tests/integration_tests.ipynb index 6c9d709..dcaa5f1 100644 --- a/tests/integration_tests.ipynb +++ b/tests/integration_tests.ipynb @@ -12,7 +12,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 2, "id": "63b5feff-aa8a-417c-8c93-9b9d74e5dee9", "metadata": {}, "outputs": [], @@ -23,7 +23,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 3, "id": "f6012705-9d34-4997-8681-c7bbcc4f008b", "metadata": {}, "outputs": [], @@ -2889,7 +2889,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 4, "id": "f5c3ed3e-13dd-4399-924e-3d1ac17ce387", "metadata": {}, "outputs": [ @@ -2998,25 +2998,23 @@ "\n", "\n", "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "Checking results for long_read_sc_test\n", - "\tExpecting: {'contig': '6', 'barcode': 'ENSMUST00000203816-AACGTGTTGGAGAGGG-16-G', 'position': 115807969, 'num_rows': 1, 'count': 1, 'coverage': 1, 'conversion': 'A>C', 'strand_conversion': 'T>G', 'strand': '-', 'feature_name': 'Rpl32'}\n", - "\n", - "\t >>> long_read_sc_test passed! <<<\n", - "\n", - "\tExpecting: {'contig': '6', 'barcode': 'ENSMUST00000081840-AAGTCGTACCAGGCTC-40-C', 'position': 115805653, 'num_rows': 1, 'count': 1, 'coverage': 1, 'conversion': 'G>A', 'strand_conversion': 'C>T', 'strand': '-', 'feature_name': 'Rpl32'}\n", - "\n", - "\t >>> long_read_sc_test passed! <<<\n", - "\n", - "\tExpecting: {'contig': '6', 'barcode': 'ENSMUST00000081840-AACGTGTTGGAGAGGG-40-G', 'position': 115807015, 'num_rows': 1, 'count': 1, 'coverage': 8, 'conversion': 'C>T', 'strand_conversion': 'G>A', 'strand': '-', 'feature_name': 'Rpl32'}\n", - "\n", - "\t >>> long_read_sc_test passed! <<<\n", - "\n", - "Checking that analyzing a single-cell dataset in 'bulk' mode (i.e. not specificying the 'CB' barcode) yields the exact same positions and base changes, but with counts and coverages aggregated rather than at a single-cell resolution\n", - "grouped_sc_rows: 62, bulk_rows: 62\n", - "\n", - "\t >>> single-cell and bulk on same dataset comparison passed! <<<\n", - "\n", - "There were 0 failures\n" + "Checking results for long_read_sc_test\n" + ] + }, + { + "ename": "FileNotFoundError", + "evalue": "[Errno 2] No such file or directory: 'singlecell_tests/long_read_sc_test/final_filtered_site_info_annotated.tsv'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[4], line 267\u001b[0m\n\u001b[1;32m 265\u001b[0m folder \u001b[38;5;241m=\u001b[39m info\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mfolder\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 266\u001b[0m final_filtered_site_info_annotated \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m/final_filtered_site_info_annotated.tsv\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mformat(folder, test_name)\n\u001b[0;32m--> 267\u001b[0m final_filtered_site_info_annotated_df \u001b[38;5;241m=\u001b[39m \u001b[43mpd\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mread_csv\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfinal_filtered_site_info_annotated\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msep\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;130;43;01m\\t\u001b[39;49;00m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindex_col\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 269\u001b[0m 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dtype_backend)\u001b[0m\n\u001b[1;32m 899\u001b[0m kwds_defaults \u001b[38;5;241m=\u001b[39m _refine_defaults_read(\n\u001b[1;32m 900\u001b[0m dialect,\n\u001b[1;32m 901\u001b[0m delimiter,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 908\u001b[0m dtype_backend\u001b[38;5;241m=\u001b[39mdtype_backend,\n\u001b[1;32m 909\u001b[0m )\n\u001b[1;32m 910\u001b[0m kwds\u001b[38;5;241m.\u001b[39mupdate(kwds_defaults)\n\u001b[0;32m--> 912\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_read\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfilepath_or_buffer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mkwds\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/miniconda3/envs/marine_environment/lib/python3.8/site-packages/pandas/io/parsers/readers.py:577\u001b[0m, in \u001b[0;36m_read\u001b[0;34m(filepath_or_buffer, kwds)\u001b[0m\n\u001b[1;32m 574\u001b[0m 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'singlecell_tests/long_read_sc_test/final_filtered_site_info_annotated.tsv'" ] } ], diff --git a/tests/singlecell_tests/scripts/long_read_sc_test.sh b/tests/singlecell_tests/scripts/long_read_sc_test.sh index ea0be8e..cea15c2 100644 --- a/tests/singlecell_tests/scripts/long_read_sc_test.sh +++ b/tests/singlecell_tests/scripts/long_read_sc_test.sh @@ -13,7 +13,7 @@ $MARINE/tests/singlecell_tests/long_read_sc_test \ 0 \ --cores \ 16 \ ---barcode_whitelist_file $MARINE/examples/data/sc_lr_barcodes.tsv.gz \ +--barcode_whitelist_file $MARINE/examples/data/sc_lr_barcodes.tsv \ --strandedness 2 \ --barcode_tag "IB" \ --contigs "6" \