#infname = 'head-data.csv' # bzgrep -m100 . /shared/silo_researcher/Matsen_F/MatsenGrp/data/bcr/output_sw/C/01-C-N_merged.tsv.bz2 | sed 's/[ \t][ \t]*/,/g'|cut -f2 -d, > head-data.csv
with opener('r')(infname) as infile:
germlines = utils.read_germlines('../../../recombinator')
reader = csv.DictReader(infile)
for inline in reader:
print 'searching'
# inline['seq'] = inline['seq'][-130:]
searcher = Searcher(inline['seq'], debug=True, n_matches_max=2)
searcher.search()
inferred_group_str = ''
true_group_str = ''
outline = {}
outline['seq'] = inline['seq']
print 'RESULT ',
for region in utils.regions:
inferred_name = searcher.get_best_match_name(region)
outline[region + '_gene'] = utils.unsanitize_name(inferred_name)
true_name = utils.sanitize_name(inline[region + '_gene'])
inferred_group_str += inferred_name
true_group_str += true_name
if inferred_name == 'none':
print ' none',
elif inferred_name == true_name:
print ' - ',
else:
print ' x ',
for region in utils.regions:
print '%3d' % searcher.n_tries[region],
print ''
print ' true'
