diff gtf_to_gff.py @ 10:c42c69aa81f8

fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gtf_to_gff.py	Thu Apr 23 18:01:45 2015 -0400
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+"""
+Convert Gene Transfer Format [GTF] to Generic Feature Format Version 3 [GFF3].
+
+Usage: python gtf_to_gff.py in.gtf > out.gff3  
+    
+Requirement:
+    GFFParser.py: https://github.com/vipints/GFFtools-GX/blob/master/GFFParser.py    
+    helper.py: https://github.com/vipints/GFFtools-GX/blob/master/helper.py
+    
+Copyright (C) 
+    2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany.
+    2012-2015 Memorial Sloan Kettering Cancer Center New York City, USA.
+"""
+
+import re
+import sys
+import helper
+import GFFParser
+
+def GFFWriter(gtf_content):
+    """
+    write the feature information to GFF format
+
+    @args gtf_content: Parsed object from gtf file 
+    @type gtf_content: numpy array
+    """
+
+    sys.stdout.write('##gff-version 3\n')
+    for ent1 in gtf_content:
+        chr_name = ent1['chr']
+        strand = ent1['strand']
+        start = ent1['start']
+        stop = ent1['stop']
+        source = ent1['source']
+        ID = ent1['name']
+        Name = ent1['gene_info']['Name']
+        Name = ID if not Name else Name 
+
+        sys.stdout.write('%s\t%s\tgene\t%d\t%d\t.\t%s\t.\tID=%s;Name=%s\n' % (chr_name, source, start, stop, strand, ID, Name))
+        for idx, tid in enumerate(ent1['transcripts']):
+
+            t_start = ent1['exons'][idx][0][0]
+            t_stop = ent1['exons'][idx][-1][-1]
+            t_type = ent1['transcript_type'][idx]
+
+            utr5_exons, utr3_exons = [], [] 
+            if ent1['exons'][idx].any() and ent1['cds_exons'][idx].any():
+                utr5_exons, utr3_exons = helper.buildUTR(ent1['cds_exons'][idx], ent1['exons'][idx], strand)
+
+            sys.stdout.write('%s\t%s\t%s\t%d\t%d\t.\t%s\t.\tID=%s;Parent=%s\n' % (chr_name, source, t_type, t_start, t_stop, strand, tid[0], ID))
+            for ex_cod in utr5_exons:
+                sys.stdout.write('%s\t%s\tfive_prime_UTR\t%d\t%d\t.\t%s\t.\tParent=%s\n' % (chr_name, source, ex_cod[0], ex_cod[1], strand, tid[0]))
+
+            for ex_cod in ent1['cds_exons'][idx]:
+                sys.stdout.write('%s\t%s\tCDS\t%d\t%d\t.\t%s\t%d\tParent=%s\n' % (chr_name, source, ex_cod[0], ex_cod[1], strand, ex_cod[2], tid[0]))
+
+            for ex_cod in utr3_exons:
+                sys.stdout.write('%s\t%s\tthree_prime_UTR\t%d\t%d\t.\t%s\t.\tParent=%s\n' % (chr_name, source, ex_cod[0], ex_cod[1], strand, tid[0]))
+
+            for ex_cod in ent1['exons'][idx]:
+                sys.stdout.write('%s\t%s\texon\t%d\t%d\t.\t%s\t.\tParent=%s\n' % (chr_name, source, ex_cod[0], ex_cod[1], strand, tid[0]))
+            
+
+def __main__():
+
+    try:
+        gtf_fname = sys.argv[1]
+    except:
+        print __doc__
+        sys.exit(-1)
+
+    gtf_file_content = GFFParser.Parse(gtf_fname)  
+
+    GFFWriter(gtf_file_content)
+
+if __name__ == "__main__": 
+    __main__()