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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,197 @@ | ||
| #!/usr/bin/env python | ||
|
|
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| import argparse | ||
| import logging | ||
| import sys | ||
| from pathlib import Path | ||
| import pandas as pd | ||
| import ast | ||
|
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| logger = logging.getLogger() | ||
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| FUSIONINSPECTOR_MAP = { | ||
| "fusion": {"column": 0, "delimiter": "\t", "element": 0}, | ||
| "chromosomeA": {"column": 7, "delimiter": ":", "element": 0}, | ||
| "chromosomeB": {"column": 10, "delimiter": ":", "element": 0}, | ||
| "posA": {"column": 7, "delimiter": ":", "element": 1}, | ||
| "posB": {"column": 10, "delimiter": ":", "element": 1}, | ||
| "strand1": {"column": 7, "delimiter": ":", "element": 2}, | ||
| "strand2": {"column": 10, "delimiter": ":", "element": 2}, | ||
| "geneA": {"column": 0, "delimiter": "--", "element": 0}, | ||
| "geneB": {"column": 0, "delimiter": "--", "element": 1}, | ||
| "split_reads": {"column": 1, "delimiter": "\t", "element": 0}, | ||
| "discordant_pairs": {"column": 2, "delimiter": "\t", "element": 0}, | ||
| "ffpm": {"column": 25, "delimiter": "\t", "element": 0}, | ||
| } | ||
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| def parse_args(argv=None): | ||
| """Define and immediately parse command line arguments.""" | ||
| parser = argparse.ArgumentParser( | ||
| description="Validate and transform a tabular samplesheet.", | ||
| epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv", | ||
| ) | ||
| parser.add_argument( | ||
| "--fusioninspector", | ||
| metavar="FUSIONINSPECTOR", | ||
| type=Path, | ||
| help="FusionInspector output in TSV format.", | ||
| ) | ||
| parser.add_argument( | ||
| "--fusionreport", | ||
| metavar="FUSIONREPORT", | ||
| type=Path, | ||
| help="Fusionreport output in TSV format.", | ||
| ) | ||
| parser.add_argument("--sample", metavar="SAMPLE", type=Path, help="Sample name.", default="Sample") | ||
| parser.add_argument( | ||
| "--out", | ||
| metavar="OUT", | ||
| type=Path, | ||
| help="Output path.", | ||
| ) | ||
| return parser.parse_args(argv) | ||
|
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|
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| def header_def(sample): | ||
| return '##fileformat=VCFv4.1\n\ | ||
| ##ALT=<ID=BND,Description="Break end">\n\ | ||
| ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n\ | ||
| ##INFO=<ID=CHRA,Number=1,Type=String,Description="Chromosome A">\n\ | ||
| ##INFO=<ID=CHRB,Number=1,Type=String,Description="Chromosome B">\n\ | ||
| ##INFO=<ID=GENEA,Number=.,Type=String,Description="Gene A">\n\ | ||
| ##INFO=<ID=GENEB,Number=.,Type=String,Description="Gene B">\n\ | ||
| ##INFO=<ID=ORIENTATION,Number=.,Type=String,Description="Strand1 and strand2 directions">\n\ | ||
| ##INFO=<ID=FOUND_DB,Number=.,Type=String,Description="Databases in which the fusion has been found">\n\ | ||
| ##INFO=<ID=ARRIBA,Number=.,Type=String,Description="Found by arriba">\n\ | ||
| ##INFO=<ID=FUSIONCATCHER,Number=.,Type=String,Description="Found by fusioncatcher">\n\ | ||
| ##INFO=<ID=PIZZLY,Number=.,Type=String,Description="Found by pizzly">\n\ | ||
| ##INFO=<ID=SQUID,Number=.,Type=String,Description="Found by squid">\n\ | ||
| ##INFO=<ID=STARFUSION,Number=.,Type=String,Description="Found by starfusion">\n\ | ||
| ##INFO=<ID=TOOL_HITS,Number=.,Type=Integer,Description="Number of tools that found the fusion">\n\ | ||
| ##INFO=<ID=SCORE,Number=.,Type=Float,Description="Score from fusionreport">\n\ | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n\ | ||
| ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of paired-ends that support the event">\n\ | ||
| ##FORMAT=<ID=RV,Number=1,Type=Integer,Description="Number of split reads that support the event">\n\ | ||
| ##FORMAT=<ID=FFPM,Number=1,Type=Float,Description="Fusion fragments per million total RNA-seq fragments">\n\ | ||
| #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t{}'.format( | ||
| sample | ||
| ) | ||
|
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|
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| def read_fusioninspector(fusioninspector_file, col_num, delimiter, element): | ||
| with open(fusioninspector_file) as fusioninspector: | ||
| return [line.split()[col_num].split(delimiter)[element] for line in fusioninspector if not line.startswith("#")] | ||
|
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| def build_fusioninspector_dataframe(file, map): | ||
| new_dict = {} | ||
| for key in FUSIONINSPECTOR_MAP: | ||
| new_dict[key] = read_fusioninspector( | ||
| file, | ||
| map[key]["column"], | ||
| map[key]["delimiter"], | ||
| map[key]["element"], | ||
| ) | ||
| return pd.DataFrame.from_dict(new_dict).set_index("fusion") | ||
|
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| def read_build_fusionreport(fusionreport_file): | ||
| with open(fusionreport_file) as fusionreport: | ||
| from_html = [line.split('rows": [')[1] for line in fusionreport if 'name="fusion_list' in line] | ||
| expression = from_html[0].split('], "tool')[0] | ||
| return pd.DataFrame.from_dict(ast.literal_eval(expression)).set_index("fusion") | ||
|
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|
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| def column_manipulation(df): | ||
| df["ALT"] = "" | ||
| df = df.reset_index() | ||
| df["FORMAT"] = "GT:DV:RV:FFPM" | ||
| df["ID"] = "." | ||
| df["QUAL"] = "." | ||
| df["FILTER"] = "PASS" | ||
| df["REF"] = "N" | ||
|
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| for index, row in df.iterrows(): | ||
| # ALT | ||
| if not row["strand1"] in ["+", "-"] or not row["strand2"] in ["+", "-"]: | ||
| df.loc[index, "ALT"] = "N[{}:{}[".format(df["chromosomeB"], row["posB"]) | ||
| elif row["strand1"] == "-" and row["strand2"] == "-": | ||
| df.loc[index, "ALT"] = "[{}:{}[N".format(row["chromosomeB"], row["posB"]) | ||
| elif row["strand1"] == "+" and row["strand2"] == "-": | ||
| df.loc[index, "ALT"] = "N]{}:{}]".format(row["chromosomeB"], row["posB"]) | ||
| elif row["strand1"] == "-" and row["strand2"] == "+": | ||
| df.loc[index, "ALT"] = "N]{}:{}]".format(row["chromosomeB"], row["posB"]) | ||
| else: | ||
| df.loc[index, "ALT"] = "N[{}:{}[".format(row["chromosomeB"], row["posB"]) | ||
| # INFO | ||
| df.loc[index, "INFO"] = ( | ||
| "SVTYPE=BND;CHRA={};CHRB={};GENEA={};GENEB={};ORIENTATION={},{};FOUND_DB={};" | ||
| "ARRIBA={};FUSIONCATCHER={};PIZZLY={};SQUID={};STARFUSION={};TOOL_HITS={};SCORE={}".format( | ||
| row["chromosomeA"], | ||
| row["chromosomeB"], | ||
| row["geneA"], | ||
| row["geneB"], | ||
| row["strand1"], | ||
| row["strand2"], | ||
| row["found_db"], | ||
| row["arriba"], | ||
| row["fusioncatcher"], | ||
| row["pizzly"], | ||
| row["squid"], | ||
| row["starfusion"], | ||
| row["tools_hits"], | ||
| row["score"], | ||
| ) | ||
| ) | ||
| # FORMAT | ||
| df.loc[index, "Sample"] = "./1:{}:{}:{}".format(row["split_reads"], row["discordant_pairs"], row["ffpm"]) | ||
| return df | ||
|
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| def write_vcf(df_to_print, header, out_file): | ||
| df_to_print[ | ||
| [ | ||
| "chromosomeA", | ||
| "posA", | ||
| "ID", | ||
| "REF", | ||
| "ALT", | ||
| "QUAL", | ||
| "FILTER", | ||
| "INFO", | ||
| "FORMAT", | ||
| "Sample", | ||
| ] | ||
| ].to_csv( | ||
| path_or_buf=out_file, | ||
| sep="\t", | ||
| header=None, | ||
| index=False, | ||
| ) | ||
|
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| with open(out_file, "r+") as f: | ||
| content = f.read() | ||
| f.seek(0, 0) | ||
| f.write(header.rstrip("\r\n") + "\n" + content) | ||
|
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| def megafusion(fusioninspector_in_file, fusionreport_in_file, sample, out): | ||
| """Convert fusion information from FusionInspector and fusion-report into a vcf file. Adapted from https://github.com/J35P312/MegaFusion""" | ||
| merged_df = build_fusioninspector_dataframe(fusioninspector_in_file, FUSIONINSPECTOR_MAP).join( | ||
| read_build_fusionreport(fusionreport_in_file), how="left" | ||
| ) | ||
| write_vcf(column_manipulation(merged_df), header_def(sample), out) | ||
|
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| def main(argv=None): | ||
| """Coordinate argument parsing and program execution.""" | ||
| args = parse_args(argv) | ||
| if not args.fusioninspector.is_file() or not args.fusionreport.is_file(): | ||
| logger.error(f"The given input file {args.fusioninspector} or {args.fusionreport} was not found!") | ||
| sys.exit(2) | ||
| megafusion(args.fusioninspector, args.fusionreport, args.sample, args.out) | ||
|
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|
|
||
| if __name__ == "__main__": | ||
| sys.exit(main()) |
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