Added initial script for merging call and region files #45
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nakib103
requested changes
Nov 11, 2025
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| logging.basicConfig(level=logging.INFO) | ||
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| def find_variant_by_accession(xml_file, accession) -> dict|None: |
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loading the XML into memory and then querying would be much faster.
The XMLs are in MB - so it should not take up much of memory.
scripts/merge_region_call.py
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| header.info.add("ALLELE_TYPE", 1, "String", "Aggregated type of supporting calls") | ||
| header.info.add("CN", ".", "String", "Comma-separated list of copy numbers of supporting calls") | ||
| if "SVLEN" not in header.info: | ||
| del header.info['SVLEN'] |
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Suggested change
| del header.info['SVLEN'] |
redundant
scripts/merge_region_call.py
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| if calls: | ||
| new_rec.info["ALLELE_NAME"] = ",".join(call["ALLELE_NAME"] for call in calls) | ||
| new_rec.info["ALLELE_TYPE"] = aggregate_sv_type(call["ALLELE_TYPE"] for call in calls) | ||
| new_rec.alts = tuple([f"<{call['ALLELE_TYPE']}>" for call in calls]) |
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Is there a reason we are calculating final alts from SVTYPE?
scripts/merge_region_call.py
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| new_rec.info["ALLELE_NAME"] = ",".join(call["ALLELE_NAME"] for call in calls) | ||
| new_rec.info["ALLELE_TYPE"] = aggregate_sv_type(call["ALLELE_TYPE"] for call in calls) | ||
| new_rec.alts = tuple([f"<{call['ALLELE_TYPE']}>" for call in calls]) | ||
| new_rec.info["SVLEN"] = ",".join(call["SVLEN"][0] for call in calls if call["SVLEN"] is not None) |
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- if there is no SVLEN we need to put a
.. As like any allele specific field SVELN needs one-to-one relationship with allele, otherwise we do not know which SVLEN belongs to which allele. - Is there a reason we are taking
call["SVLEN"][0](I assume for call there is always one allele and the list will always contain single value?)
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Hi @nakib103 , call["SVLEN"] is giving a list of single value (as opposed to the value itself) because of the type of SVLEN in VCF header.
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NW-70