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Deduplicate records and CPX variant IDs in ResolveComplexVariants (#576)
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src/sv-pipeline/04_variant_resolution/scripts/integrate_resolved_vcfs.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,103 @@ | ||
| #!/bin/env python | ||
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| import argparse | ||
| import sys | ||
| from typing import Optional, List, Text, Dict, Set, Callable | ||
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| import pysam | ||
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| MEMBERS_KEY = "MEMBERS" | ||
| UNRESOLVED_KEY = "UNRESOLVED" | ||
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| def update_header(header: pysam.VariantHeader) -> None: | ||
| header.add_line('##INFO=<ID=UNRESOLVED,Number=0,Type=Flag,Description="Variant is unresolved.">') | ||
| header.add_line('##INFO=<ID=UNRESOLVED_TYPE,Number=1,Type=String,Description=\"Class of unresolved variant.\">') | ||
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| def is_unresolved(record: pysam.VariantRecord): | ||
| return record.info.get(UNRESOLVED_KEY, None) | ||
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| def is_resolved(record: pysam.VariantRecord): | ||
| return not is_unresolved(record) | ||
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| def get_members(record: pysam.VariantRecord): | ||
| return list(record.info[MEMBERS_KEY]) if isinstance(record.info[MEMBERS_KEY], tuple) \ | ||
| else [record.info[MEMBERS_KEY]] if record.info[MEMBERS_KEY] is not None \ | ||
| else list() | ||
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| def get_vids_and_members_sets(vcf: pysam.VariantFile, | ||
| predicate: Callable) -> Dict: | ||
| unresolved_vids_set = set() | ||
| unresolved_members_set = set() | ||
| for r in vcf: | ||
| if predicate(r): | ||
| unresolved_vids_set.add(r.id) | ||
| unresolved_members_set.update(get_members(r)) | ||
| vcf.reset() | ||
| return unresolved_vids_set, unresolved_members_set | ||
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| def write_vcf(header: pysam.VariantHeader, | ||
| all_vcf: pysam.VariantFile, | ||
| inv_vcf: pysam.VariantFile, | ||
| inv_resolved_vids_set: Set, | ||
| inv_resolved_members_set: Set, | ||
| all_unresolved_vids_set: Set, | ||
| all_unresolved_members_set: Set) -> None: | ||
| sys.stdout.write(str(header)) | ||
| for r in all_vcf: | ||
| if r.id not in all_unresolved_vids_set or r.id not in inv_resolved_members_set: | ||
| # Resolved in ALL vcf, or unresolved in both VCFs | ||
| sys.stdout.write(str(r)) | ||
| for r in inv_vcf: | ||
| if r.id in inv_resolved_vids_set: | ||
| # Resolved variant in the INV vcf | ||
| members = get_members(r) | ||
| if all((m in all_unresolved_members_set) for m in members): | ||
| # Resolved in the INV vcf and every member unresolved in the ALL vcf | ||
| sys.stdout.write(str(r)) | ||
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| def __parse_arguments(argv: List[Text]) -> argparse.Namespace: | ||
| # noinspection PyTypeChecker | ||
| parser = argparse.ArgumentParser( | ||
| description="Integrates inversion-only and all-SV VCFs from the complex resolve module. " | ||
| "Unsorted output is written to stdout.", | ||
| formatter_class=argparse.ArgumentDefaultsHelpFormatter | ||
| ) | ||
| parser.add_argument("--all-vcf", type=str, required=True, | ||
| help="Complex-resolved VCF containing all SVs") | ||
| parser.add_argument("--inv-only-vcf", type=str, required=True, | ||
| help="Complex-resolved VCF containing only inversions") | ||
| if len(argv) <= 1: | ||
| parser.parse_args(["--help"]) | ||
| sys.exit(0) | ||
| parsed_arguments = parser.parse_args(argv[1:]) | ||
| return parsed_arguments | ||
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| def main(argv: Optional[List[Text]] = None): | ||
| if argv is None: | ||
| argv = sys.argv | ||
| arguments = __parse_arguments(argv) | ||
| with pysam.VariantFile(arguments.all_vcf) as all_vcf, \ | ||
| pysam.VariantFile(arguments.inv_only_vcf) as inv_vcf: | ||
| header = all_vcf.header | ||
| update_header(header) | ||
| inv_resolved_vids_set, inv_resolved_members_set = get_vids_and_members_sets(inv_vcf, is_resolved) | ||
| all_unresolved_vids_set, all_unresolved_members_set = get_vids_and_members_sets(all_vcf, is_unresolved) | ||
| write_vcf(header=header, | ||
| all_vcf=all_vcf, | ||
| inv_vcf=inv_vcf, | ||
| inv_resolved_vids_set=inv_resolved_vids_set, | ||
| inv_resolved_members_set=inv_resolved_members_set, | ||
| all_unresolved_vids_set=all_unresolved_vids_set, | ||
| all_unresolved_members_set=all_unresolved_members_set) | ||
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| if __name__ == "__main__": | ||
| main() |
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