def should_to_tap_one_file(f_should):
f_tap = f_should + PROG_TAG + TAP_SUFFIX
f_tap = f_tap.replace(SHOULD_SUFFIX, '')
f_log = f_should + PROG_TAG + LOG_SUFFIX
f_log = f_log.replace(SHOULD_SUFFIX, '')
f_vdj = f_should + PROG_TAG + '.vdj'
f_vdj = f_vdj.replace(SHOULD_SUFFIX, '')
print "<== %s" % f_should
vdj = repseq_vdj.VDJ_File()
vdj.parse_from_gen(repseq_vdj.should_results_from_vidjil(args.program.replace('{directory}',args.directory), f_should, f_log))
print "==> %s" % f_vdj
vdj.write(open(f_vdj, 'w'))
write_should_results_to_tap(vdj, f_tap)
tap_line = should_result_to_tap(should, result, tap_id + 1)
if tap_line is not None:
if args.verbose or '#!' in tap_line:
print tap_line
ff.write(tap_line + '\n')
if __name__ == '__main__':
for f_should in args.file:
if '.vdj' in f_should:
f_vdj = f_should
f_tap = f_vdj + TAP_SUFFIX
vdj = repseq_vdj.VDJ_File()
vdj.parse_from_file(open(f_vdj))
write_should_results_to_tap(vdj, f_tap)
continue
should_to_tap_one_file(f_should)
if args.revcomp:
f_should_rc = f_should + '.rc'
os.system('python ../../germline/revcomp-fasta.py < %s > %s' %
(f_should, f_should_rc))
should_to_tap_one_file(f_should_rc)
print
print "=== Summary, should-vdj tests ===" + (' (only locus)'
if args.after_two else '')