Commit 7dee03d2 authored by Mathieu Giraud's avatar Mathieu Giraud option '-q', launching only Vidjil (Multi)KmerSegmenter

We launch here something like 'vidjil -c windows -uU'.
parent fa43c1e0
......@@ -20,8 +20,12 @@ from subprocess import Popen, PIPE, STDOUT
import os
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--program', '-p', default='../../vidjil -c segment -i -g ../../germline %s > %s', help='program to launch on each file (%(default)s)')
VIDJIL_FINE = '../../vidjil -c segment -i -g ../../germline %s > %s'
VIDJIL_KMER = '../../vidjil -b out -c windows -uU -i -g ../../germline %s > /dev/null ; cat out/out.segmented.vdj.fa out/out.unsegmented.vdj.fa > %s'
parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('--program', '-p', default=VIDJIL_FINE, help='program to launch on each file (%(default)s)')
parser.add_argument('-q', dest='program', action='store_const', const=VIDJIL_KMER, help='shortcut for -p (VIDJIL_KMER), to be used with -2')
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('file', nargs='+', help='''.should-vdj.fa files''')
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