def test_get_first_id(self):
"""get_first_id should identify first id in fasta file"""
lines = """>S74_1 E86FECS01CEVAV orig_bc=ACATGTCACGTG new_bc=ACATGTCACGTG bc_diffs=0
CTCCTC
>Unassigned_2 E86FECS01EKKMF orig_bc=AGCGCTGATGTA new_bc=None bc_diffs=1
GGTGCCTCCCTCGC
>S80_3 E86FECS01EKKMF orig_bc=AGCGCTGATGTA new_bc=None bc_diffs=1
GGTGCCTCCCTCGC
>S80_4 E86FECS01CW66X orig_bc=AGTCCATAGCTG new_bc=AGTCCATAGCTG bc_diffs=0
GTCCTGGCAG""".splitlines()
self.assertEqual(get_first_id(lines), set(["S74_1", "Unassigned_2", "S80_3", "S80_4"]))
def test_get_first_id(self):
"""get_first_id should identify first id in fasta file"""
lines = """>S74_1 E86FECS01CEVAV orig_bc=ACATGTCACGTG new_bc=ACATGTCACGTG bc_diffs=0
CTCCTC
>Unassigned_2 E86FECS01EKKMF orig_bc=AGCGCTGATGTA new_bc=None bc_diffs=1
GGTGCCTCCCTCGC
>S80_3 E86FECS01EKKMF orig_bc=AGCGCTGATGTA new_bc=None bc_diffs=1
GGTGCCTCCCTCGC
>S80_4 E86FECS01CW66X orig_bc=AGTCCATAGCTG new_bc=AGTCCATAGCTG bc_diffs=0
GTCCTGGCAG""".splitlines()
self.assertEqual(get_first_id(lines), set(['S74_1','Unassigned_2','S80_3','S80_4']))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
options, args = option_parser.parse_args()
if options.debug:
print "PRODUCING DEBUG OUTPUT"
bad_seq_ids = set()
bad_otu_ids = None
# if we got a file to screen against, find the relevant ids and delete them
if options.screened_rep_seqs:
bad_otu_ids = get_first_id(open(options.screened_rep_seqs, 'U'))
if not options.otus:
raise RuntimeError(
"Must specify an OTU file if performing a screen.")
for line in open(options.otus, 'U'):
fields = line.split()
if fields[0] in bad_otu_ids:
bad_seq_ids.update(fields[1:])
if options.debug:
if bad_otu_ids is not None:
print "Found %s bad otu ids: %s" % (len(bad_otu_ids), bad_otu_ids)
print "Found %s bad seq ids: %s" % (len(bad_seq_ids), bad_seq_ids)
ids = get_ids(open(options.in_fasta, 'U'), options.field, bad_seq_ids,
options.debug)
# add empty unassigned ids for file creation
if 'Unassigned' not in ids:
ids['Unassigned'] = []
if not exists(options.outdir):
makedirs(options.outdir)
for k, idlist in ids.items():
outfile = open(join(options.outdir, k + '.txt'), 'w')
outfile.write('\n'.join(sorted(idlist)))
outfile.close()
