1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
|
#!/usr/bin/env python
import argparse
import logging
import csv
import sys
import re
from Bio import SeqIO
log = logging.getLogger(__name__)
description_regexp = re.compile(r'([^\s_]+)_\d+\s+(\S+)')
def main():
logging.basicConfig(
level=logging.INFO, format="%(levelname)s: %(message)s")
parser = argparse.ArgumentParser(
description="Extract the original sequence names from a QIIME FASTA file.")
parser.add_argument(
'qiime', type=argparse.FileType('r'), nargs='?', default=sys.stdin,
help="input QIIME file (default: stdin)")
parser.add_argument(
'fasta', type=argparse.FileType('w'), nargs='?', default=sys.stdout,
help="output FASTA file (default: stdout)")
parser.add_argument(
'specimen_map', type=argparse.FileType('w'), nargs='?',
help="if specified, output specimen map (default: don't write)")
args = parser.parse_args()
specimen_writer = None
if args.specimen_map is not None:
specimen_writer = csv.writer(args.specimen_map)
for seq in SeqIO.parse(args.qiime, 'fasta'):
match = description_regexp.match(seq.description)
if not match:
log.warning("sequence %r had a strange description", seq.id)
continue
specimen, seq.id = match.groups()
seq.description = ''
SeqIO.write([seq], args.fasta, 'fasta')
if specimen_writer:
specimen_writer.writerow((seq.id, specimen))
main()
|
