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removing professor status from cat
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ksamuk committed Apr 2, 2020
1 parent adf2552 commit 107402e
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion pixy/__main__.py
Original file line number Diff line number Diff line change
Expand Up @@ -96,7 +96,7 @@ def main(args=None):
chrom_all = chrom_list
else:
chrom_list = list(args.chromosomes.split(","))
chrom_all = subprocess.check_output(cat_prof + args.vcf + " | grep -v '#' | awk '{print $1}' | uniq", shell=True).decode("utf-8").split()
chrom_all = subprocess.check_output(cat_prog + args.vcf + " | grep -v '#' | awk '{print $1}' | uniq", shell=True).decode("utf-8").split()
missing = list(set(chrom_list)-set(chrom_all))
if len(missing) >0:
raise Exception('ERROR: the following chromosomes were requested but not occur in the VCF:', missing)
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