def test_filter_bridge_and_reverse(self):
fna = list(ep.read_fasta("test.fna"))
bridge_filt = epic_barcoder.filter_bridge(
fna, '16S', 'GWATTACCGCGGCKGCTGCATCTTCTCCAAATGGGTCATGATC')
bridge_reverse_filt = epic_barcoder.filter_reverse(
bridge_filt, 'ATTAGAWACCCBDGTAGTCC')
self.assertEqual(len(list(bridge_reverse_filt)), 13)
def split_seqs(seq_file, no_splits):
seqs = ep.read_fasta(seq_file)
split_dict = make_split_dict(seqs, no_splits)
for key, val in split_dict.items():
seq_name = key + "_tmp.fasta"
ep.write_fasta(val, seq_name)
return list(split_dict.keys())
def add_otus_to_fasta(seq_file, uc_file, output_file):
seeds = get_seed_dict(uc_file)
seq_acc = []
for seq_id, seq in ep.read_fasta(seq_file):
short_id = seq_id[1:].split()[0]
seed_id = seeds[short_id]
new_seq_id = "{} OTU={}".format(seq_id.strip(), seed_id)
seq_acc.append([new_seq_id, seq])
ep.write_fasta(seq_acc, output_file)
def test_process_barcode_info(self):
epic_barcoder.process_barcode_info(
"test.fna", "tmp.fasta", '16S',
'GWATTACCGCGGCKGCTGCATCTTCTCCAAATGGGTCATGATC',
'ATTAGAWACCCBDGTAGTCC')
tmp_fna = list(ep.read_fasta("tmp.fasta"))
os.remove("tmp.fasta")
self.assertEqual(
[len(seq) for _, seq in tmp_fna],
[249, 249, 250, 250, 249, 249, 249, 250, 250, 250, 250, 249, 250])
def process_barcode_info(bc_seq,
output_file,
bridge_seq,
reverse_seq=None,
seq_type=None):
bc_lst = ep.read_fasta(bc_seq)
bridge_filtered = filter_bridge(bc_lst, seq_type, bridge_seq)
if reverse_seq:
out_iter = filter_reverse(bridge_filtered, reverse_seq)
ep.write_fasta(out_iter, output_file)
else:
ep.write_fasta(bridge_filtered, output_file)
def test_filter_bridge(self):
fna = list(ep.read_fasta("test.fna"))
filt = list(
epic_barcoder.filter_bridge(
fna, '16S', 'GWATTACCGCGGCKGCTGCATCTTCTCCAAATGGGTCATGATC'))
self.assertEqual(len(filt), 25)
def test_filter_reverse(self):
fna = list(ep.read_fasta("test.fna"))
filt = list(epic_barcoder.filter_reverse(fna, 'ATTAGAWACCCBDGTAGTCC'))
self.assertEqual(len(filt), 34)