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Remove PyVCF dependency #19

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Remove PyVCF dependency #19

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2 changes: 1 addition & 1 deletion examples/brca.vcf
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@
##contig=<ID=chrY,length=59373566>
##INFO=<ID=AF_ESP,Number=1,Type=Float,Description="allele frequencies from GO-ESP">
#CHROM POS ID REF ALT QUAL FILTER INFO
chr17 41276135 . TTAA GTCT . . .
chr17 41276135 . TTAA GTCT . . .
chr17 41276135 . T G . . .
chr17 41276135 . T C . . .
chr17 41276135 . T A . . .
Expand Down
57 changes: 38 additions & 19 deletions pangolin/pangolin.py
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Original file line number Diff line number Diff line change
@@ -1,12 +1,13 @@
import argparse
from pkg_resources import resource_filename
from pangolin.model import *
import vcf

import gffutils
import pandas as pd
import pyfastx
# import time
# startTime = time.time()
import pysam
from pkg_resources import resource_filename

from pangolin.model import *


IN_MAP = np.asarray([[0, 0, 0, 0],
[1, 0, 0, 0],
Expand Down Expand Up @@ -240,20 +241,38 @@ def main():
if line[0] != '#':
break

variants = vcf.Reader(filename=variants)
variants.infos["Pangolin"] = vcf.parser._Info(
"Pangolin",'.',"String","Pangolin splice scores. "
"Format: gene|pos:score_change|pos:score_change|warnings,...",'.','.')
fout = vcf.Writer(open(args.output_file+".vcf", 'w'), variants)

for i, variant in enumerate(variants):
scores = process_variant(lnum+i, str(variant.CHROM), int(variant.POS), variant.REF, str(variant.ALT[0]), gtf, models, args)
if scores != -1:
variant.INFO["Pangolin"] = scores
fout.write_record(variant)
fout.flush()

fout.close()
with pysam.VariantFile(variants) as variant_file, pysam.VariantFile(
args.output_file+".vcf", "w", header=variant_file.header
) as out_variant_file:
out_variant_file.header.add_meta(
key="INFO",
items=[
("ID", "Pangolin"),
("Number", "."),
("Type", "String"),
(
"Description",
"Pangolin splice scores. Format: gene|pos:score_change|pos:score_change|warnings,..."
),
]
)
for i, variant_record in enumerate(variant_file):
variant_record.translate(out_variant_file.header)
assert variant_record.ref, f"Empty REF field in variant record {variant_record}"
assert variant_record.alts, f"Empty ALT field in variant record {variant_record}"
scores = process_variant(
lnum + i,
str(variant_record.contig),
int(variant_record.pos),
variant_record.ref,
str(variant_record.alts[0]),
gtf,
models,
args,
)
if scores != -1:
variant_record.info["Pangolin"] = scores
out_variant_file.write(variant_record)

elif variants.endswith(".csv"):
col_ids = args.column_ids.split(',')
Expand Down