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
48
49
|
#!/usr/bin/env python
from string import strip
from cogent.parse.fasta import MinimalFastaParser
__author__ = "Jesse Zaneveld"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jesse Zaneveld", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Jesse Zaneveld"
__email__ = "zaneveld@gmail.com"
__status__ = "Production"
"""
Parser for KEGG fasta files
This code is useful for parsing the KEGG .nuc or .pep files
"""
def parse_fasta(lines):
"""lightweight parser for KEGG FASTA format sequences"""
for label, seq in MinimalFastaParser(lines):
yield '\t'.join(list(kegg_label_fields(label)) \
+ [seq] + ["\n"])
def kegg_label_fields(line):
"""Splits line into KEGG label fields.
Format is species:gene_id [optional gene_name]; description.
"""
fields = map(strip, line.split(None, 1))
id_ = fields[0]
species, gene_id = map(strip, id_.split(':',1))
#check if we got a description
gene_name = description = ''
if len(fields) > 1:
description = fields[1]
if ';' in description:
gene_name, description = map(strip, description.split(';',1))
return id_, species, gene_id, gene_name, description
if __name__ == '__main__':
from sys import argv
filename = argv[1]
for result_line in parse_fasta(open(filename)):
print result_line.strip()
|
