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43 lines
1.1 KiB
Python
43 lines
1.1 KiB
Python
#!/usr/bin/env python
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from Bio import GenBank
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import sys, os, textwrap
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assert sys.version_info[:2] >= ( 2, 4 )
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def make_fasta(rec):
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'''Creates fasta format from a record'''
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gi = rec.annotations.get('gi','')
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org = rec.annotations.get('organism','')
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date = rec.annotations.get('date','')
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head = '>gi:%s, id:%s, org:%s, date:%s\n' % (gi, rec.id, org, date)
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body = '\n'.join(textwrap.wrap(rec.seq.data, width=80))
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return head, body
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if __name__ == '__main__':
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mode = sys.argv[1]
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text = sys.argv[2]
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output_file = sys.argv[3]
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print 'Searching for %s <br>' % text
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# check if inputs are all numbers
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try:
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gi_list = text.split()
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tmp = map(int, gi_list)
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except ValueError:
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gi_list = GenBank.search_for(text, max_ids=10)
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fp = open(output_file, 'wt')
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record_parser = GenBank.FeatureParser()
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ncbi_dict = GenBank.NCBIDictionary(mode, 'genbank', parser = record_parser)
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for gid in gi_list:
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res = ncbi_dict[gid]
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head, body = make_fasta(res)
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fp.write(head+body+'\n')
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print head
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fp.close()
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