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change a regex to allow gene names with underscore #1

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change a regex to allow gene names with underscore #1

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2 changes: 1 addition & 1 deletion ogs_merge/ogs_merge
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Original file line number Diff line number Diff line change
Expand Up @@ -489,7 +489,7 @@ class OgsMerger():
# FIXME CDS could be more appropriate (or maybe not...)
if not li.startswith("#") and cols[2] == 'exon':
cols[8] = re.sub(r'ID=([a-zA-Z0-9]+)', r'exID=\1', cols[8]) # remove already set id
cols[8] = re.sub(r'Parent=([a-zA-Z0-9]+)([\.0-9]+)?([-_]R[A-Z]+)?(,[a-zA-Z0-9\.\-_]*)?', r'ID=\1', cols[8]) # generate a fake id based on Parent + remove multiple parents (ie when an exon is part of multiple isoforms)
cols[8] = re.sub(r'Parent=([a-zA-Z0-9_]+)([\.0-9]+)?([-_]R[A-Z]+)?(,[a-zA-Z0-9\.\-_]*)?', r'ID=\1', cols[8]) # generate a fake id based on Parent + remove multiple parents (ie when an exon is part of multiple isoforms)
cols[8] = cols[8].rstrip(";") # gff2bed doesn't like trailing ;
print('\t'.join(cols), file=base_gff_out)
base_gff_out.close()
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