Mercurial > repos > xuebing > sharplabtool
comparison tools/data_source/genbank.py @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 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 |