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DKI/convert_to_vcf #21

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May 27, 2024
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DKI/convert_to_vcf #21

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d79310e
vcf
May 13, 2024
463edaf
trailing lines in refactoring.py
May 13, 2024
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29 changes: 29 additions & 0 deletions data_collection/refactoring.py
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Original file line number Diff line number Diff line change
Expand Up @@ -125,3 +125,32 @@ def from_clinvar_name_to_cdna_position(name):
break

return name[start:end]


def save_lovd_as_vcf(df, save_to):
"""
Gets hg38 variants from LOVD and saves as VCF file.
:param DataFrame df: LOVD DataFrame with data
:param str save_to: path where to save VCF file.
"""

if "VariantOnGenome/DNA/hg38" not in df.columns:
raise ValueError("VariantOnGenome/DNA/hg38 is not in the LOVD DataFrame.")

save_to_dir = os.path.dirname(save_to)
if not os.path.exists(save_to_dir):
os.makedirs(save_to_dir)

with open(save_to, "w", encoding="UTF-8") as f:
header = ("##fileformat=VCFv4.2\n"
"##contig=<ID=6,length=63719980>\n"
"#CHROM POS ID REF ALT QUAL FILTER INFO\n")
f.write(header)
for variant in df.loc[:, "VariantOnGenome/DNA/hg38"]:
if len(variant) != 13 or variant[-2] != '>':
logging.warning("Skipping variant %s", variant)
continue
record = ["6", variant[2:-3], ".", variant[-3], variant[-1], ".", ".", "."]

f.write("\t".join(record))
f.write("\n")
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