Commit 2096b1a6 authored by Mikaël Salson's avatar Mikaël Salson

should-vdj-to-tap.py: Ignore CDR3

parent 959c556b
......@@ -38,6 +38,7 @@ parser.add_argument('--ignore_del', '-s', action='store_true', help='ignore numb
parser.add_argument('--ignore_allele', '-A', action='store_true', help='ignore allele, checking only gene names')
parser.add_argument('--ignore_D', '-D', action='store_true', help='ignore D gene names and alleles')
parser.add_argument('--ignore_incomplete', '-+', action='store_true', help='ignore incomplete/unusual germlines')
parser.add_argument('--ignore_cdr3', '-3', action='store_true', help='ignore CDR3')
parser.add_argument('--after-two', '-2', action='store_true', help='compare only the right part of the pattern after two underscores (locus code)')
parser.add_argument('--revcomp', '-r', action='store_true', help='duplicate the tests on reverse-complemented files')
parser.add_argument('--directory', '-d', default='../..', help='base directory where Vidjil is. This value is used by the default -p and -q values (%(default)s)')
......@@ -98,6 +99,8 @@ def should_pattern_to_regex(p):
if term.startswith('{'):
term = term.replace('*','[*]').replace('!','#')
term = term.replace('{', '.*[{].*').replace('}', '.*[}]')
if args.ignore_cdr3:
term = '('+term+')?'
return [term]
# deletion/insertion/deletion
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment