--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/data_source/genbank.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+from Bio import GenBank
+import sys, os, textwrap
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def make_fasta(rec):
+    '''Creates fasta format from a record'''
+    gi   = rec.annotations.get('gi','')
+    org  = rec.annotations.get('organism','')
+    date = rec.annotations.get('date','')
+    head = '>gi:%s, id:%s, org:%s, date:%s\n' % (gi, rec.id, org, date)
+    body = '\n'.join(textwrap.wrap(rec.seq.data, width=80))
+    return head, body
+    
+if __name__ == '__main__':
+    
+    mode  = sys.argv[1]
+    text  = sys.argv[2]
+    output_file = sys.argv[3]
+
+    print 'Searching for %s <br>' % text
+    
+    # check if inputs are all numbers
+    try:
+        gi_list = text.split()
+        tmp = map(int, gi_list)
+    except ValueError:
+        gi_list = GenBank.search_for(text, max_ids=10)
+    
+    fp = open(output_file, 'wt')
+    record_parser = GenBank.FeatureParser()
+    ncbi_dict = GenBank.NCBIDictionary(mode, 'genbank', parser = record_parser)
+    for gid in gi_list:
+        res = ncbi_dict[gid]
+        head, body =  make_fasta(res)
+        fp.write(head+body+'\n')
+        print head
+    fp.close()
+
+   
+