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Remove chromosome/scaffold name mangling for bed/vcf files #137

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Merged
evancofer merged 3 commits into from
Feb 11, 2020
Merged

Remove chromosome/scaffold name mangling for bed/vcf files #137

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f6fe0d9
Removed chromosome chr-based filtering
evancofer Jan 28, 2020
38b6c08
Replaced automatic addition of chr- for VEP
evancofer Jan 28, 2020
9a0aee6
Added prepending of 'chr' based on ref seq
evancofer Feb 7, 2020
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10 changes: 9 additions & 1 deletion selene_sdk/predict/_variant_effect_prediction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,11 @@ def read_vcf_file(input_path,
"""
variants = []
na_rows = []
check_chr = True
for chrom in reference_sequence.get_chrs():
if not chrom.startswith("chr"):
check_chr = False
break
with open(input_path, 'r') as file_handle:
lines = file_handle.readlines()
index = 0
Expand All @@ -85,12 +90,15 @@ def read_vcf_file(input_path,
chrom = str(cols[0])
if 'CHR' == chrom[:3]:
chrom = chrom.replace('CHR', 'chr')
elif "chr" not in chrom:
elif "chr" not in chrom and check_chr is True:
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@kathyxchen kathyxchen Feb 9, 2020

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update to 'chr' not in chrom and check_chr

chrom = "chr" + chrom

if chrom == "chrMT" and \
chrom not in reference_sequence.get_chrs():
chrom = "chrM"
elif chrom == "MT" and \
chrom not in reference_sequence.get_chrs():
chrom = "M"

pos = int(cols[1])
name = cols[2]
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9 changes: 7 additions & 2 deletions selene_sdk/predict/model_predict.py
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Original file line number Diff line number Diff line change
Expand Up @@ -298,6 +298,11 @@ def _get_sequences_from_bed_file(self,
sequences = []
labels = []
na_rows = []
check_chr = True
for chrom in reference_sequence.get_chrs():
if not chrom.startswith("chr"):
check_chr = False
break
with open(input_path, 'r') as read_handle:
for i, line in enumerate(read_handle):
cols = line.strip().split('\t')
Expand All @@ -310,8 +315,8 @@ def _get_sequences_from_bed_file(self,
strand = '.'
if isinstance(strand_index, int) and len(cols) > strand_index:
strand = cols[strand_index]
if 'chr' not in chrom:
chrom = 'chr{0}'.format(chrom)
if 'chr' not in chrom and check_chr is True:
chrom = "chr{0}".format(chrom)
if not str.isdigit(start) or not str.isdigit(end) \
or chrom not in self.reference_sequence.genome:
na_rows.append(line)
Expand Down