--- a/tRNAscan.py	Wed Jul 26 10:14:05 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-#!/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 -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:])