diff gff_to_gtf.py @ 5:6e589f267c14

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gff_to_gtf.py	Tue Nov 04 12:15:19 2014 -0500
@@ -0,0 +1,76 @@
+#!/usr/bin/env python 
+"""
+Program to convert data from GFF to GTF 
+
+Usage: python gff_to_gtf.py in.gff > out.gtf 
+
+Requirement:
+    GFFParser.py: https://github.com/vipints/GFFtools-GX/blob/master/GFFParser.py    
+
+Copyright (C) 
+    2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany.
+    2012-2014 Memorial Sloan Kettering Cancer Center New York City, USA.
+"""
+
+import re
+import sys
+import GFFParser
+
+def printGTF(tinfo):
+    """
+    writing result file in GTF format
+
+    @args tinfo: parsed object from gff file
+    @type tinfo: numpy array 
+    """
+
+    for ent1 in tinfo:
+        for idx, tid in enumerate(ent1['transcripts']):
+            
+            exons = ent1['exons'][idx]
+            cds_exons = ent1['cds_exons'][idx]
+
+            stop_codon = start_codon = ()
+
+            if ent1['strand'] == '+':
+                if cds_exons.any():
+                    start_codon = (cds_exons[0][0], cds_exons[0][0]+2) 
+                    stop_codon = (cds_exons[-1][1]-2, cds_exons[-1][1]) 
+            elif ent1['strand'] == '-':
+                if cds_exons.any():
+                    start_codon = (cds_exons[-1][1]-2, cds_exons[-1][1])
+                    stop_codon = (cds_exons[0][0], cds_exons[0][0]+2)
+            else:
+                print 'STRAND information missing - %s, skip the transcript - %s' % (ent1['strand'], tid[0]) 
+                pass 
+                
+            last_cds_cod = 0 
+            for idz, ex_cod in enumerate(exons):
+
+                print '%s\t%s\texon\t%d\t%d\t.\t%s\t.\tgene_id "%s"; transcript_id "%s"; exon_number "%d"; gene_name "%s"; ' % (ent1['chr'], ent1['source'], ex_cod[0], ex_cod[1], ent1['strand'], ent1['name'], tid[0], idz+1, ent1['gene_info']['Name'])
+
+                if cds_exons.any():
+                    try:
+                        print '%s\t%s\tCDS\t%d\t%d\t.\t%s\t%d\tgene_id "%s"; transcript_id "%s"; exon_number "%d"; gene_name "%s"; ' % (ent1['chr'], ent1['source'], cds_exons[idz][0], cds_exons[idz][1], ent1['strand'], cds_exons[idz][2], ent1['name'], tid[0], idz+1, ent1['gene_info']['Name'])
+                        last_cds_cod = idz 
+                    except:
+                        pass 
+
+                    if idz == 0:
+                        print '%s\t%s\tstart_codon\t%d\t%d\t.\t%s\t%d\tgene_id "%s"; transcript_id "%s"; exon_number "%d"; gene_name "%s"; ' % (ent1['chr'], ent1['source'], start_codon[0], start_codon[1], ent1['strand'], cds_exons[idz][2], ent1['name'], tid[0], idz+1, ent1['gene_info']['Name'])
+
+            if stop_codon:
+                print '%s\t%s\tstop_codon\t%d\t%d\t.\t%s\t%d\tgene_id "%s"; transcript_id "%s"; exon_number "%d"; gene_name "%s"; ' % (ent1['chr'], ent1['source'], stop_codon[0], stop_codon[1], ent1['strand'], cds_exons[last_cds_cod][2], ent1['name'], tid[0], idz+1, ent1['gene_info']['Name'])
+
+    
+if __name__ == "__main__": 
+
+    try:
+        gff_fname = sys.argv[1]
+    except:
+        print __doc__
+        sys.exit(-1)
+
+    Transcriptdb = GFFParser.Parse(gff_fname)  
+
+    printGTF(Transcriptdb)