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1 # -*- coding: utf-8 -*-
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2 """
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3 Glimmer --> anomaly
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4 version 0.2 (andrea.pinna@crs4.it)
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5 """
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6
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7 import optparse
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8 import subprocess
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9 import sys
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10
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11 def __main__():
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12 # load arguments
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13 print 'Parsing Anomaly input options...'
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14 parser = optparse.OptionParser()
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15 parser.add_option('--anSequence', dest='sequence', help='')
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16 parser.add_option('--anCoords', dest='coords', help='')
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17 parser.add_option('--anCheckFirstCodon', action='store_true', dest='check_first_codon', help='')
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18 parser.add_option('--anCheckStopCodon', action='store_true', dest='check_stop_codon', help='')
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19 parser.add_option('--anStartCodons', dest='start_codons', help='')
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20 parser.add_option('--anStopCodons', dest='stop_codons', help='')
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21 parser.add_option('--anOutput', dest='output', help='')
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22 parser.add_option('--logfile', dest='logfile', help='')
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23 (options, args) = parser.parse_args()
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24 if len(args) > 0:
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25 parser.error('Wrong number of arguments')
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26
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27 # build Anomaly command to be executed
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28 # sequence file
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29 sequence = options.sequence
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30 coords = options.coords
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31 if options.start_codons:
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32 start_codons = '-A %s' % (options.start_codons)
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33 else:
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34 start_codons = ''
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35 if options.stop_codons:
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36 stop_codons = '-Z %s' % (options.stop_codons)
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37 else:
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38 stop_codons = ''
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39 if options.check_first_codon:
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40 check_first_codon = '-s'
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41 else:
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42 check_first_codon = ''
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43 if options.check_stop_codon:
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44 check_stop_codon = '-t'
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45 else:
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46 check_stop_codon = ''
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47 output = options.output
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48 logfile = options.logfile
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49
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50 # Build Anomaly command
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51 cmd = 'anomaly %s %s %s %s %s %s > %s' % (start_codons, check_first_codon, check_stop_codon, stop_codons, sequence, coords, output)
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52 print '\nAnomaly command to be executed: \n %s' % (cmd)
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53
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54 print 'Executing Anomaly...'
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55 if logfile:
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56 log = open(logfile, 'w')
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57 else:
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58 log = sys.stdout
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59 try:
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60 subprocess.check_call(cmd, stdout=log, stderr=subprocess.STDOUT, shell=True)
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61 finally:
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62 if log != sys.stdout:
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63 log.close()
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64 print 'Anomaly executed!'
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65
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66
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67 if __name__ == "__main__":
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68 __main__()
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