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1 # -*- coding: utf-8 -*-
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2 """
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3 Glimmer --> glimmer3
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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 shutil
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9 import subprocess
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10 import sys
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11
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12 def __main__():
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13 # load arguments
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14 print 'Parsing input options...'
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15 parser = optparse.OptionParser()
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16 parser.add_option('--glSequence', dest='sequence', help='')
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17 parser.add_option('--glIcm', dest='icm', help='')
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18 #parser.add_option('--glPrefix', dest='prefix', help='')
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19 parser.add_option('--glStartCodons', dest='start_codons', help='')
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20 parser.add_option('--glRbsPwm', dest='rbs_pwm', help='')
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21 parser.add_option('--glGcPercent', dest='gc_percent', type='float', help='')
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22 parser.add_option('--glEntropy', dest='entropy', help='')
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23 parser.add_option('--glFirstCodon', action='store_true', dest='first_codon', help='')
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24 parser.add_option('--glGeneLen', dest='gene_len', type='int', help='')
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25 parser.add_option('--glIgnore', dest='ignore', help='')
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26 parser.add_option('--glLinear', action='store_true', dest='linear', help='')
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27 parser.add_option('--glOrfCoords', dest='orf_coords', help='')
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28 parser.add_option('--glSeparateGenes', action='store_true', dest='separate_genes', help='')
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29 parser.add_option('--glMaxOverlap', dest='max_olap', type='int', help='')
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30 parser.add_option('--glStartProbs', dest='start_probs', help='')
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31 parser.add_option('--glIgnoreScoreLen', dest='ignore_score_len', type='int', help='')
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32 parser.add_option('--glNoIndep', action='store_true', dest='no_indep', help='')
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33 parser.add_option('--glThreshold', dest='threshold', type='int', help='')
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34 parser.add_option('--glExtend', action='store_true', dest='extend', help='')
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35 parser.add_option('--glTransTable', dest='trans_table', type='int', help='')
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36 parser.add_option('--glStopCodons', dest='stop_codons', help='')
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37 parser.add_option('--glDetail', dest='detail', help='')
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38 parser.add_option('--glPredict', dest='predict', help='')
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39 parser.add_option('--logfile', dest='logfile', help='')
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40 (options, args) = parser.parse_args()
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41 if len(args) > 0:
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42 parser.error('Wrong number of arguments')
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43
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44 # build Glimmer3 command to be executed
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45 # sequence file
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46 sequence = options.sequence
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47 # icm file
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48 icm = options.icm
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49 # prefix (not needed)
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50 prefix = 'prefix'
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51 # start codons
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52 if options.start_codons:
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53 start_codons = '--start_codons %s' % (options.start_codons)
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54 else:
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55 start_codons = ''
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56 # rbs_pwm
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57 if options.rbs_pwm:
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58 rbs_pwm = '--rbs_pwm %s' % (options.rbs_pwm)
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59 else:
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60 rbs_pwm = ''
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61 # gc percentage
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62 if options.gc_percent is not None:
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63 gc_percent = '--gc_percent %s' % (options.gc_percent)
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64 else:
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65 gc_percent = ''
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66 # entropy
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67 if options.entropy:
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68 entropy = "--entropy '%s'" % (options.entropy)
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69 else:
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70 entropy = ''
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71 # first_codon
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72 if options.first_codon:
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73 first_codon = '--first_codon'
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74 else:
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75 first_codon = ''
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76 # gene length
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77 if options.gene_len is not None:
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78 gene_len = '--gene_len %d' % (options.gene_len)
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79 else:
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80 gene_len = ''
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81 # ignore
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82 if options.ignore:
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83 ignore = '--ignore %s' % (options.ignore)
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84 else:
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85 ignore = ''
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86 # linear
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87 if options.linear:
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88 linear = '--linear'
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89 else:
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90 linear = ''
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91 # orf_coords
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92 if options.orf_coords:
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93 orf_coords = '--orf_coords %s' % (options.orf_coords)
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94 else:
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95 orf_coords = ''
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96 # separate genes
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97 if options.separate_genes:
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98 separate_genes = '--separate_genes'
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99 else:
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100 separate_genes = ''
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101 # max overlap
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102 if options.max_olap is not None:
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103 max_olap = '--max_olap %d' % (options.max_olap)
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104 else:
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105 max_olap = ''
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106 # start probs
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107 if options.start_probs:
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108 start_probs = '--start_probs %s' % (options.start_probs)
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109 else:
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110 start_probs = ''
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111 # ignore score length
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112 if options.ignore_score_len is not None:
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113 ignore_score_len = '--ignore_score_len %d' % (options.ignore_score_len)
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114 else:
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115 ignore_score_len = ''
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116 # no indep
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117 if options.no_indep:
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118 no_indep = '--no_indep'
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119 else:
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120 no_indep = ''
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121 # threshold
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122 if options.threshold is not None:
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123 threshold = '--threshold %d' % (options.threshold)
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124 else:
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125 threshold = ''
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126 # extend
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127 if options.extend:
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128 extend = '--extend'
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129 else:
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130 extend = ''
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131 # trans table
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132 if options.trans_table is not None:
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133 trans_table = '--trans_table %d' % (options.trans_table)
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134 else:
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135 trans_table = ''
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136 # stop codons
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137 if options.stop_codons:
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138 stop_codons = '--stop_codons %s' % (options.stop_codons)
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139 else:
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140 stop_codons = ''
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141 logfile = options.logfile
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142
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143 # Build Glimmer3 command
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144 cmd = 'glimmer3 %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s' % (start_codons, rbs_pwm, gc_percent, entropy, first_codon, gene_len, ignore, linear, orf_coords, separate_genes, max_olap, start_probs, ignore_score_len, no_indep, threshold, extend, trans_table, stop_codons, sequence, icm, prefix)
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145 print '\nGlimmer3 command to be executed: \n %s' % (cmd)
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146
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147 print 'Executing Glimmer3...'
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148 if logfile:
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149 log = open(logfile, 'w')
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150 else:
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151 log = sys.stdout
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152 try:
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153 subprocess.check_call(cmd, stdout=log, stderr=subprocess.STDOUT, shell=True)
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154 finally:
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155 if log != sys.stdout:
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156 log.close()
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157 print 'Glimmer3 executed!'
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158
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159 shutil.move(prefix + ".detail", options.detail)
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160 shutil.move(prefix + ".predict", options.predict)
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161
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162
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163 if __name__ == "__main__":
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164 __main__()
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