# HG changeset patch
# User kellrott
# Date 1371141627 14400
# Node ID b849537e6f691faa950db4480dea130ea48100f7

Uploaded

diff -r 000000000000 -r b849537e6f69 gaf2gtf/gaf2gtf.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gaf2gtf/gaf2gtf.py	Thu Jun 13 12:40:27 2013 -0400
@@ -0,0 +1,148 @@
+#!/usr/bin/env python
+
+import sys
+import os
+
+COL_ENTRY_NUMBER = 0
+COL_FEATURE_ID = 1
+COL_FEATURE_TYPE = 2
+COL_FEATURE_DB_SOURCE = 3
+COL_FEATURE_DB_VERSION = 4
+COL_FEATURE_DB_DATE = 5
+COL_FEATURE_SEQ_FILENAME = 6
+COL_COMPOSITE_ID = 7
+COL_COMPOSITE_TYPE = 8
+COL_COMPOSITE_DB_SOURCE = 9
+COL_COMPOSITE_DB_VERSION = 10
+COL_COMPOSITE_DB_DATE = 11
+COL_ALIGNMENT_TYPE = 12
+COL_FEATURE_COORDINATES = 13
+COL_COMPOSITE_COORDINATES = 14
+COL_GENE = 15
+COL_GENE_LOCUS = 16
+COL_FEATURE_ALIASES = 17
+COL_FEATURE_INFO = 18
+
+
+if __name__ == "__main__":
+	if sys.argv[1] == "-":
+		src_name = "stdin" 
+		handle = sys.stdin
+	else:		
+		src_name = os.path.basename(sys.argv[1])
+		handle = open(sys.argv[1])
+	ohandle = sys.stdout
+	
+	for line in handle:
+		if not line.startswith("#"):
+			row = line.rstrip().split("\t")
+			#only working on genes right now
+			if row[COL_FEATURE_TYPE] == "gene":		
+				
+				#use the composite coordinates to create an array of exons, and 
+				#calculate the frame windows for the different exons
+				seq_str = row[COL_COMPOSITE_COORDINATES]
+				chrome, locs, strand = seq_str.split(":")
+				pos_list = []
+				if strand == '+':
+					cds_pos = 0
+					for span in locs.split(","):
+						start, stop = span.split("-")
+						pos_list.append( (start, stop, cds_pos) )
+						cds_pos += int(stop) + 1 - int(start)
+				elif strand == '-':
+					#for the reverse strand, we'll have to do this backwards, then 
+					#flip the results
+					cds_pos = 0
+					tmp = locs.split(",")
+					tmp.reverse()
+					for span in tmp:
+						start, stop = span.split("-")
+						pos_list.append( (start, stop, cds_pos) )
+						cds_pos += int(stop) + 1 - int(start)
+					pos_list.reverse()
+				
+				#cycle through each exon and output a CDS and exon entry
+				for i, pos in enumerate(pos_list):
+					start, stop, cds_pos = pos
+					
+					kv = [
+						["gene_id", row[COL_FEATURE_ID]],
+						["transcript_id", row[COL_FEATURE_ID]],
+						["exon_number", str(i+1)],
+						["exon_id", "%s.%d" % (row[COL_FEATURE_ID], i+1)]						
+					]
+					
+					#generate the key-value array to be put into attributes field
+					kv_prep = ( "%s \"%s\"" % (a[0], a[1]) for a in kv )
+					
+					out = [
+						chrome,
+						src_name,
+						"exon",
+						start,
+						stop,
+						".",
+						strand,
+						".",
+						"; ".join(kv_prep)
+					]					
+					ohandle.write("%s\n" % ("\t".join(out)))
+					out[2] = "CDS"
+					out[7] = "%d" % ( (3 - (cds_pos % 3)) % 3 )
+					ohandle.write("%s\n" % ("\t".join(out)))
+					
+				#output the cds_start and cds_end fields using the gene locations
+				seq_str = row[COL_GENE_LOCUS]
+				if seq_str.count(";") == 0:
+					chrome, span, strand = seq_str.split(":")
+					gene_start, gene_stop = span.split("-")
+					
+					kv = [
+						["gene_id", row[COL_FEATURE_ID]],
+						["transcript_id", row[COL_FEATURE_ID]],
+						["exon_number", str(i+1)],
+						["exon_id", "%s.%d" % (row[COL_FEATURE_ID], i+1)]						
+					]
+						
+					kv_prep = ( "%s \"%s\"" % (a[0], a[1]) for a in kv )
+					kv_str = "; ".join(kv_prep)
+					out = [
+						chrome,
+						src_name,
+						"start_codon",
+						"0",
+						"0",
+						".",
+						strand,
+						"0",
+						kv_str
+					]				
+					if strand == '+':
+						out[3] = gene_start
+						out[4] = str(int(gene_start) + 2)
+					else:
+						out[3] = str(int(gene_stop) - 2)
+						out[4] = gene_stop
+					ohandle.write("%s\n" % ("\t".join(out)))
+	
+					out = [
+						chrome,
+						src_name,
+						"stop_codon",
+						"0",
+						"0",
+						".",
+						strand,
+						"0",
+						kv_str
+					]
+					if strand == '+':
+						out[3] = str(int(gene_stop) + 1 - 2)
+						out[4] = str(int(gene_stop) + 1)
+					else:
+						out[3] = str(int(gene_start) - 2)
+						out[4] = str(int(gene_start))
+					ohandle.write("%s\n" % ("\t".join(out)))
+	
+					
diff -r 000000000000 -r b849537e6f69 gaf2gtf/gaf2gtf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gaf2gtf/gaf2gtf.xml	Thu Jun 13 12:40:27 2013 -0400
@@ -0,0 +1,16 @@
+<tool id="gaf2gtf" name="gaf2gtf" version="0.1.0">
+	<description>Convert TCGA GAF file to a GTF file</description>
+	<command interpreter="python">gaf2gtf.py $gaf_file > $gtf_file</command>
+	<inputs>
+		<param name="gaf_file" type="data" label="TCGA GAF File"/>
+	</inputs>
+	<outputs>
+		<data format="gtf" name="gtf_file" label="GTF file"/>
+	</outputs>
+	<help>
+A GAF file can be found at 
+
+https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/other/GAF/GAF.hg19.June2011.bundle/outputs/TCGA.hg19.June2011.gaf
+
+	</help>
+</tool>