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1 #!/usr/bin/env python
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2
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3 """
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4
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5 Converts tRNAScan output back to fasta-sequences.
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6
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7 """
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8
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9 import sys
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10 from Bio import SeqIO
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11 from Bio.SeqRecord import SeqRecord
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12 import subprocess
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13
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14
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15 def main(args):
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16 """
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17 Call from galaxy:
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18 tRNAscan.py $organism $mode $showPrimSecondOpt $disablePseudo $showCodons $tabular_output $inputfile $fasta_output
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19
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20 tRNAscan-SE $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -d -Q -y -q -b -o $tabular_output $inputfile;
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21 """
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22 cmd = """tRNAscan-SE -Q -y -q -b %s""" % ' '.join( args[:-1] )
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23 child = subprocess.Popen(cmd.split(),
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24 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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25 stdout, stderr = child.communicate()
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26 return_code = child.returncode
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27 if return_code:
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28 sys.stdout.write(stdout)
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29 sys.stderr.write(stderr)
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30 sys.stderr.write("Return error code %i from command:\n" % return_code)
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31 sys.stderr.write("%s\n" % cmd)
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32 else:
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33 sys.stdout.write(stdout)
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34 sys.stdout.write(stderr)
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35
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36 outfile = args[-1]
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37 sequence_file = args[-2]
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38 tRNAScan_file = args[-3]
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39
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40 with open( sequence_file ) as sequences:
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41 sequence_recs = SeqIO.to_dict(SeqIO.parse(sequences, "fasta"))
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42
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43 tRNAs = []
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44 with open(tRNAScan_file) as tRNA_handle:
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45 for line in tRNA_handle:
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46 line = line.strip()
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47 if not line or line.startswith('#'):
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48 continue
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49 cols = line.split()
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50 iid = cols[0].strip()
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51 start = int(cols[2])
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52 end = int(cols[3])
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53 aa = cols[4]
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54 codon = cols[5]
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55 rec = sequence_recs[ iid ]
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56 if start > end:
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57 new_rec = rec[end:start]
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58 new_rec.seq = new_rec.seq.reverse_complement()
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59 new_rec.description = "%s %s %s %s %s" % (rec.description, aa, codon, start, end)
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60 new_rec.id = rec.id
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61 new_rec.name = rec.name
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62 tRNAs.append( new_rec )
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63 else:
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64 new_rec = rec[start:end]
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65 new_rec.id = rec.id
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66 new_rec.name = rec.name
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67 new_rec.description = "%s %s %s %s %s" % (rec.description, aa, codon, start, end)
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68 tRNAs.append( new_rec )
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69
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70 SeqIO.write(tRNAs, open(outfile, 'w+'), "fasta")
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71
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72
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73 if __name__ == '__main__':
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74 main(sys.argv[1:])
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