diff gff_to_gbk.py @ 5:6e589f267c14

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gff_to_gbk.py	Tue Nov 04 12:15:19 2014 -0500
@@ -0,0 +1,54 @@
+#!/usr/bin/env python 
+"""
+Convert data from GFF and associated genome sequence in fasta file into GenBank.
+
+Usage: 
+python gff_to_gbk.py in.gff in.fasta out.gbk 
+
+Requirements:
+    BioPython:- http://biopython.org/
+    helper.py : https://github.com/vipints/GFFtools-GX/blob/master/helper.py
+
+Copyright (C) 
+    2010-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany.
+    2012-2014 Memorial Sloan Kettering Cancer Center New York City, USA.
+"""
+
+import sys
+import helper
+import gffparser_bcbio
+
+from Bio import SeqIO
+from Bio.Alphabet import generic_dna
+
+def __main__():
+    """
+    main wrapper
+    """
+
+    try:
+        gff_fname = sys.argv[1]
+        fasta_fname = sys.argv[2]
+        gb_fname = sys.argv[3]
+    except: 
+        print __doc__
+        sys.exit(-1)
+
+    fasta_fh = helper.open_file(fasta_fname) 
+
+    fasta_rec = SeqIO.to_dict(SeqIO.parse(fasta_fh, "fasta", generic_dna))
+    fasta_fh.close()
+
+    gff_rec = gffparser_bcbio.parse(gff_fname, fasta_rec)
+    
+    try:
+        gb_fh = open(gb_fname, "w")
+    except:
+        print 'file not ready for writing %s' % gb_fname
+        sys.exit(-1)
+
+    SeqIO.write(gff_rec, gb_fh, "genbank")
+    gb_fh.close()
+
+if __name__=="__main__":
+    __main__()