--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tRNAscan.py	Sat Jul 06 10:37:13 2013 -0400
@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+
+"""
+    Converts tRNAScan output back to fasta-sequences.
+"""
+import sys
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+import subprocess
+
+
+def main(args):
+    """
+        Call from galaxy:
+        tRNAscan.py $organism $mode $showPrimSecondOpt $disablePseudo $showCodons $tabular_output $inputfile $fasta_output
+
+            tRNAscan-SE $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -d -Q -y -q -b -o $tabular_output $inputfile;
+    """
+    cmd = """tRNAscan-SE -Q -y -q -b %s""" % ' '.join( args[:-1] )
+    child = subprocess.Popen(cmd.split(),
+        stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    stdout, stderr = child.communicate()
+    return_code = child.returncode
+    if return_code:
+        sys.stdout.write(stdout)
+        sys.stderr.write(stderr)
+        sys.stderr.write("Return error code %i from command:\n" % return_code)
+        sys.stderr.write("%s\n" % cmd)
+    else:
+        sys.stdout.write(stdout)
+        sys.stdout.write(stderr)
+
+    outfile = args[-1]
+    sequence_file = args[-2]
+    tRNAScan_file = args[-3]
+
+    with open( sequence_file ) as sequences:
+        sequence_recs = SeqIO.to_dict(SeqIO.parse(sequences, "fasta"))
+
+    tRNAs = []
+    with open(tRNAScan_file) as tRNA_handle:
+        for line in tRNA_handle:
+            line = line.strip()
+            if not line or line.startswith('#'):
+                continue
+            cols = line.split()
+            iid = cols[0].strip()
+            start = int(cols[2])
+            end = int(cols[3])
+            aa = cols[4]
+            codon = cols[5]
+            rec = sequence_recs[ iid ]
+            if start > end:
+                new_rec = rec[end:start]
+                new_rec.seq = new_rec.seq.reverse_complement()
+                new_rec.description = "%s %s %s %s %s" % (rec.description, aa, codon, start, end)
+                new_rec.id = rec.id
+                new_rec.name = rec.name
+                tRNAs.append( new_rec )
+            else:
+                new_rec = rec[start:end]
+                new_rec.id = rec.id
+                new_rec.name = rec.name
+                new_rec.description = "%s %s %s %s %s" % (rec.description, aa, codon, start, end)
+                tRNAs.append( new_rec )
+
+    SeqIO.write(tRNAs, open(outfile, 'w+'), "fasta")
+
+
+if __name__ == '__main__':
+    main(sys.argv[1:])