--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bed_to_gff.py	Thu Apr 23 18:01:45 2015 -0400
@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+"""
+Convert genome annotation data in a 12 column BED format to GFF3. 
+
+Usage: 
+    python bed_to_gff.py in.bed > out.gff
+
+Requirement:
+    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 
+
+def __main__():
+    """
+    main function 
+    """
+
+    try:
+        bed_fname = sys.argv[1]
+    except:
+        print __doc__
+        sys.exit(-1)
+
+    bed_fh = helper.open_file(bed_fname)
+
+    for line in bed_fh: 
+        line = line.strip( '\n\r' )
+
+        if not line or line[0] in  ['#']:
+            continue 
+
+        parts = line.split('\t') 
+        assert len(parts) >= 12, line
+
+        rstarts = parts[-1].split(',')
+        rstarts.pop() if rstarts[-1] == '' else rstarts
+
+        exon_lens = parts[-2].split(',')
+        exon_lens.pop() if exon_lens[-1] == '' else exon_lens
+        
+        if len(rstarts) != len(exon_lens):
+            continue # checking the consistency col 11 and col 12 
+
+        if len(rstarts) != int(parts[-3]): 
+            continue # checking the number of exons and block count are same
+        
+        if not parts[5] in ['+', '-']:
+            parts[5] = '.' # replace the unknown strand with '.' 
+
+        # bed2gff result line 
+        sys.stdout.write('%s\tbed2gff\tgene\t%d\t%s\t%s\t%s\t.\tID=Gene:%s;Name=Gene:%s\n' % (parts[0], int(parts[1])+1, parts[2], parts[4], parts[5], parts[3], parts[3]))
+        sys.stdout.write('%s\tbed2gff\ttranscript\t%d\t%s\t%s\t%s\t.\tID=%s;Name=%s;Parent=Gene:%s\n' % (parts[0], int(parts[1])+1, parts[2], parts[4], parts[5], parts[3], parts[3], parts[3]))
+
+        st = int(parts[1])
+        for ex_cnt in range(int(parts[-3])):
+            start = st + int(rstarts[ex_cnt]) + 1
+            stop = start + int(exon_lens[ex_cnt]) - 1
+            sys.stdout.write('%s\tbed2gff\texon\t%d\t%d\t%s\t%s\t.\tParent=%s\n' % (parts[0], start, stop, parts[4], parts[5], parts[3]))
+
+    bed_fh.close()
+
+
+if __name__ == "__main__": 
+    __main__()