-
Notifications
You must be signed in to change notification settings - Fork 32
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'master' into cleanup_discard_list
- Loading branch information
Showing
32 changed files
with
717 additions
and
229 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| #!/usr/bin/env bash | ||
| # | ||
| # Generates an output BigBed file from a single input BED file, | ||
| # correcting for errors. bedToBigBed errors on variants > 255 characters. | ||
| # This script removes those problem variants until bedToBigBed succeeds | ||
| # | ||
| set -o errexit | ||
|
|
||
| INPUT_BED=$1 | ||
| AS=$2 | ||
| CHROM_SIZES=$3 | ||
| OUTPUT_BIGBED=$4 | ||
|
|
||
| sort -k1,1 -k2,2 ${INPUT_BED} -o ${INPUT_BED} | ||
|
|
||
| set +e | ||
|
|
||
| # captures the first error message if present | ||
| ERROR=`bedToBigBed -type=bed9+ -as=${AS} -tab ${INPUT_BED} ${CHROM_SIZES} ${OUTPUT_BIGBED} 2>&1` | ||
|
|
||
| # parses line number of the first problem variant from the error message | ||
| ERRORLINE=`echo $ERROR | sed -n -e 's/^.*line //p' | sed 's/\s.*$//'` | ||
|
|
||
| until [ -z "$ERRORLINE" ] | ||
| do | ||
| # removes error variant | ||
| sed -i "${ERRORLINE}d" ${INPUT_BED} | ||
| echo $ERROR | ||
|
|
||
| # captures and parses the line number of the next problem variant | ||
| ERROR=`bedToBigBed -type=bed9+ -as=${AS} -tab ${INPUT_BED} ${CHROM_SIZES} ${OUTPUT_BIGBED} 2>&1` | ||
| ERRORLINE=`echo $ERROR | sed -n -e 's/^.*line //p' | sed 's/\s.*$//'` | ||
| echo $ERRORLINE | ||
| done | ||
|
|
||
| set -e | ||
|
|
||
| bedToBigBed -type=bed9+ -as=${AS} -tab ${INPUT_BED} ${CHROM_SIZES} ${OUTPUT_BIGBED} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| #!/usr/bin/env python | ||
| from collections import namedtuple, OrderedDict | ||
| import html | ||
| import genomeBrowserUtils | ||
|
|
||
|
|
||
|
|
||
|
|
||
| def _write_auto_sql_file(as_path): | ||
| with open(as_path, "w") as asFh: | ||
|
|
||
| sql = """table brcaExchanges | ||
| " These data are in BigBed bed9 format, and include selected fields from https://brcaexchange.org" | ||
| ( | ||
| string chrom; "Chromosome (or contig, scaffold, etc.)" | ||
| uint chromStart; "Start position in chromosome" | ||
| uint chromEnd; "End position in chromosome" | ||
| string name; "Name of item" | ||
| uint score; "Score from 0-1000" | ||
| char[1] strand; "+ or -" | ||
| uint thickStart; "Start of where display should be thick (start codon)" | ||
| uint thickEnd; "End of where display should be thick (stop codon)" | ||
| uint reserved; "Used as itemRgb as of 2004-11-22" | ||
| string outlink; "Link to the variant in BRCA Exchange" | ||
| string symbol; "Gene Symbol" | ||
| string cdna_hgvs; "Variant ID in cDNA HGVS nomenclature" | ||
| string protein_hgvs; "Variant ID in protein HGVS nomenclature" | ||
| string CA_ID; "ClinGen Allele Registry ID" | ||
| string provisional_evidence_code; "Provisional ACMG code" | ||
| string provional_code_description; "Accompanying description" | ||
| string _mouseOver; "mouse over field hidden" | ||
| ) | ||
| """ | ||
|
|
||
| asFh.write(sql) | ||
| print("wrote as file to {}".format(asFh.name)) | ||
|
|
||
|
|
||
| def write_track_item(rec, start, end, output_fp): | ||
| chrom = "chr"+rec.Chr | ||
| score = 0 | ||
| strand = "." | ||
| name = rec.pyhgvs_cDNA[0:254] | ||
| if name == "?": | ||
| assert(False) | ||
| thickStart = start | ||
| thickEnd = end | ||
| acmgCode = rec.Provisional_Evidence_Code_Popfreq | ||
| color = genomeBrowserUtils.acmgCodeToColor(acmgCode) | ||
| out_url = "https://brcaexchange.org/variant/" + rec.CA_ID | ||
| # | ||
| # When generating the mouseOver, truncate the strings to 50 characters each, | ||
| # to not overhwelm the browser's internal limit of 255 characters. | ||
| description = "Click on the track item for more details" | ||
| mouseOver = (("<b>Provisional ACMG Evidence Code:</b> %s<br>" + \ | ||
| "<b>Details:</b> %s") \ | ||
| % (acmgCode, description))[:245] + "<br>" | ||
| outRow = [chrom, start, end, name, score, strand, thickStart, thickEnd, color, out_url, | ||
| rec.Gene_Symbol, | ||
| genomeBrowserUtils.displayString(rec.pyhgvs_cDNA[0:254]), | ||
| genomeBrowserUtils.displayString(rec.pyhgvs_Protein[0:254]), | ||
| genomeBrowserUtils.displayString(rec.CA_ID), | ||
| acmgCode, description[:254], | ||
| mouseOver] | ||
| outRow = [str(x) for x in outRow] | ||
| output_fp.write("\t".join(outRow)+"\n") | ||
|
|
||
|
|
||
| def main(): | ||
| args = genomeBrowserUtils._get_args() | ||
|
|
||
| with open(args.input, 'r') as ifh: | ||
| ofhg19v = open(args.output_hg19_var, 'w') | ||
| ofhg38v = open(args.output_hg38_var, 'w') | ||
| ofhg19sv = open(args.output_hg19_sv, 'w') | ||
| ofhg38sv = open(args.output_hg38_sv, 'w') | ||
| print("Reading %s..." % ifh.name) | ||
|
|
||
| headers = ifh.readline().rstrip("\n").rstrip("\r").strip().split("\t") | ||
| rowRec = namedtuple("rec", headers) | ||
|
|
||
| _write_auto_sql_file(args.auto_sql_file) | ||
|
|
||
| for line in ifh: | ||
| row = line.rstrip("\n").rstrip("\r").split("\t") | ||
| rec = rowRec(*row) | ||
| rd = OrderedDict(zip(headers, row)) # row as dict | ||
| if int(rec.Hg38_End) - int(rec.Hg38_Start) < args.length_threshold: | ||
| write_track_item(rec, str(int(rec.pyhgvs_Hg37_Start)-1), rec.pyhgvs_Hg37_End, ofhg19v) | ||
| write_track_item(rec, str(int(rec.Hg38_Start)-1), rec.Hg38_End, ofhg38v) | ||
| else: | ||
| write_track_item(rec, str(int(rec.pyhgvs_Hg37_Start)-1), rec.pyhgvs_Hg37_End, ofhg19sv) | ||
| write_track_item(rec, str(int(rec.Hg38_Start)-1), rec.Hg38_End, ofhg38sv) | ||
|
|
||
| print("wrote to %s and %s" % (ofhg19v.name, ofhg38v.name)) | ||
|
|
||
|
|
||
| if __name__ == '__main__': | ||
| main() |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.