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1 # -*- coding: utf-8 -*-
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2 """
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3 Glimmer --> long-orfs
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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 Long-ORFs input options...'
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14 parser = optparse.OptionParser()
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15 parser.add_option('--loSequence', dest='sequence', help='')
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16 parser.add_option('--loStartCodons', dest='start_codons', help='')
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17 parser.add_option('--loEntropy', dest='entropy', help='')
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18 parser.add_option('--loFixed', action='store_true', dest='fixed', help='')
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19 parser.add_option('--loMinLen', dest='min_len', type='int', help='')
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20 parser.add_option('--loIgnore', dest='ignore', help='')
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21 parser.add_option('--loLinear', action='store_true', dest='linear', help='')
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22 parser.add_option('--loLengthOpt', action='store_true', dest='length_opt', help='')
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23 parser.add_option('--loNoHeader', action='store_true', dest='no_header', help='')
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24 parser.add_option('--loMaxOverlap', dest='max_olap', type='int', help='')
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25 parser.add_option('--loCutoff', dest='cutoff', type='float', help='')
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26 parser.add_option('--loWithoutStops', action='store_true', dest='without_stops', help='')
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27 parser.add_option('--loTransTable', dest='trans_table', type='int', help='')
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28 parser.add_option('--loStopCodons', dest='stop_codons', help='')
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29 parser.add_option('--loOutput', dest='output', help='')
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30 parser.add_option('--logfile', dest='logfile', help='')
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31 (options, args) = parser.parse_args()
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32 if len(args) > 0:
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33 parser.error('Wrong number of arguments')
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34
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35 # build Long-ORFs command to be executed
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36 sequence = options.sequence
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37 if options.start_codons:
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38 start_codons = '--start_codons %s' % (options.start_codons)
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39 else:
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40 start_codons = ''
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41 if options.entropy:
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42 entropy = '--entropy %s' % (options.entropy)
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43 else:
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44 entropy = ''
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45 if options.fixed:
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46 fixed = '--fixed'
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47 else:
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48 fixed = ''
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49 if options.min_len is not None:
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50 min_len = '--min_len %d' % (options.min_len)
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51 else:
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52 min_len = ''
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53 if options.ignore:
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54 ignore = '--ignore %s' % (options.ignore)
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55 else:
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56 ignore = ''
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57 if options.linear:
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58 linear = '--linear'
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59 else:
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60 linear = ''
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61 if options.length_opt:
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62 length_opt = '--length_opt'
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63 else:
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64 length_opt = ''
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65 if options.no_header:
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66 no_header = '--no_header'
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67 else:
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68 no_header = ''
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69 if options.max_olap is not None:
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70 max_olap = '--max_olap %d' % (options.max_olap)
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71 else:
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72 max_olap = ''
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73 if options.cutoff is not None:
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74 cutoff = '--cutoff %s' % (options.cutoff)
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75 else:
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76 cutoff = ''
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77 if options.without_stops:
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78 without_stops = '--without_stops'
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79 else:
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80 without_stops = ''
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81 if options.trans_table is not None:
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82 trans_table = '--trans_table %s' % (options.trans_table)
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83 else:
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84 trans_table = ''
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85 if options.stop_codons:
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86 stop_codons = '--stop_codons %s' % (options.stop_codons)
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87 else:
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88 stop_codons = ''
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89 output = options.output
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90 logfile = options.logfile
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91
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92 # Build Long-ORFs command
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93 cmd = 'long-orfs %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s' % (sequence, start_codons, entropy, fixed, min_len, ignore, linear, length_opt, no_header, max_olap, cutoff, without_stops, trans_table, stop_codons, output)
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94 print '\nLong-ORFs command to be executed: \n %s' % (cmd)
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95
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96 print 'Executing Long-ORFs...'
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97 if logfile:
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98 log = open(logfile, 'w')
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99 else:
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100 log = sys.stdout
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101 try:
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102 subprocess.check_call(cmd, stdout=log, stderr=subprocess.STDOUT, shell=True)
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103 finally:
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104 if log != sys.stdout:
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105 log.close()
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106 print 'Long-ORFs executed!'
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107
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108
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109 if __name__ == "__main__":
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110 __main__()
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