|
0
|
1 #!/usr/bin/env python
|
|
|
2 from Bio import GenBank
|
|
|
3 import sys, os, textwrap
|
|
|
4
|
|
|
5 assert sys.version_info[:2] >= ( 2, 4 )
|
|
|
6
|
|
|
7 def make_fasta(rec):
|
|
|
8 '''Creates fasta format from a record'''
|
|
|
9 gi = rec.annotations.get('gi','')
|
|
|
10 org = rec.annotations.get('organism','')
|
|
|
11 date = rec.annotations.get('date','')
|
|
|
12 head = '>gi:%s, id:%s, org:%s, date:%s\n' % (gi, rec.id, org, date)
|
|
|
13 body = '\n'.join(textwrap.wrap(rec.seq.data, width=80))
|
|
|
14 return head, body
|
|
|
15
|
|
|
16 if __name__ == '__main__':
|
|
|
17
|
|
|
18 mode = sys.argv[1]
|
|
|
19 text = sys.argv[2]
|
|
|
20 output_file = sys.argv[3]
|
|
|
21
|
|
|
22 print 'Searching for %s <br>' % text
|
|
|
23
|
|
|
24 # check if inputs are all numbers
|
|
|
25 try:
|
|
|
26 gi_list = text.split()
|
|
|
27 tmp = map(int, gi_list)
|
|
|
28 except ValueError:
|
|
|
29 gi_list = GenBank.search_for(text, max_ids=10)
|
|
|
30
|
|
|
31 fp = open(output_file, 'wt')
|
|
|
32 record_parser = GenBank.FeatureParser()
|
|
|
33 ncbi_dict = GenBank.NCBIDictionary(mode, 'genbank', parser = record_parser)
|
|
|
34 for gid in gi_list:
|
|
|
35 res = ncbi_dict[gid]
|
|
|
36 head, body = make_fasta(res)
|
|
|
37 fp.write(head+body+'\n')
|
|
|
38 print head
|
|
|
39 fp.close()
|
|
|
40
|
|
|
41
|
|
|
42
|
