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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31 """Select the transcript such that a tag value is not less than a given threshold"""
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32 import os
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33 import sys
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34 from optparse import OptionParser
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35 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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36 from commons.core.writer import MySqlTranscriptWriter
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37 from commons.core.writer.Gff3Writer import Gff3Writer
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38 from SMART.Java.Python.misc.Progress import Progress
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39 from SMART.Java.Python.misc.RPlotter import RPlotter
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40
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41 class SelectByTag(object):
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42
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43 def __init__(self, verbosity = 1):
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44 self.input = None
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45 self.format = None
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46 self.tag = None
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47 self.value = None
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48 self.min = None
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49 self.max = None
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50 self.default = None
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51 self.output = None
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52 self.mysql = None
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53 self.verbosity = verbosity
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54
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55 self.parser = None
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56 self.writer = None
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57 self.mysqlWriter = None
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58 self.nbElements = None
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59 self.nbWritten = 0
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60
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61
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62 def setParser(self):
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63 self.parser = TranscriptContainer(self.input, self.format, self.verbosity)
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64 self.nbElements = self.parser.getNbTranscripts()
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65
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66
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67 def setWriter(self):
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68 self.writer = Gff3Writer(self.output, self.verbosity)
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69 if self.mysql:
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70 self.mysqlWriter = MySqlTranscriptWriter(self.output, self.verbosity)
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71
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72
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73 def isAccepted(self, transcript):
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74 value = transcript.getTagValue(self.tag)
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75 if value == None:
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76 if self.default != None:
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77 value = self.default
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78 else:
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79 raise Exception("Error! Transcript %s no tag called '%s'" % (transcript, self.tag))
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80 if self.value != None:
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81 if self.value == str(value):
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82 return True
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83 return self.value.isdigit() and value == float(self.value)
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84 value = float(value)
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85 return (self.min == None or self.min <= value) and (self.max == None or self.max >= value)
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86
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87
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88 def readInputFile(self):
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89 progress = Progress(self.parser.getNbTranscripts(), "Writing transcripts", self.verbosity)
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90 for transcript in self.parser.getIterator():
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91 if self.isAccepted(transcript):
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92 self.writer.addTranscript(transcript)
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93 if self.mysql:
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94 self.mysqlWriter.addTranscript(transcript)
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95 self.nbWritten += 1
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96 progress.inc()
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97 progress.done()
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98
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99
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100 def writeFile(self):
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101 self.writer.write()
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102 if self.mysql:
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103 self.mysqlWriter.write()
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104
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105
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106 def run(self):
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107 self.setParser()
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108 self.setWriter()
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109 self.readInputFile()
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110 self.writeFile()
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111 if self.verbosity > 0:
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112 print "%d input" % (self.nbElements)
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113 if self.nbElements != 0:
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114 print "%d output (%.2f%%)" % (self.nbWritten, float(self.nbWritten) / self.nbElements * 100)
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115
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116
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117
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118 if __name__ == "__main__":
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119
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120 # parse command line
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121 description = "Select by Tag v1.0.2: Keep the genomic coordinates such that a the value of a given tag is between two limits. [Category: Data Selection]"
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122
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123 parser = OptionParser(description = description)
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124 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
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125 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input [compulsory] [format: transcript file format]")
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126 parser.add_option("-g", "--tag", dest="tag", action="store", default=None, type="string", help="the tag [compulsory] [format: string]")
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127 parser.add_option("-a", "--value", dest="value", action="store", default=None, type="string", help="the value to be found [format: string]")
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128 parser.add_option("-m", "--min", dest="min", action="store", default=None, type="float", help="the minimum threshold [format: float]")
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129 parser.add_option("-M", "--max", dest="max", action="store", default=None, type="float", help="the maximum threshold [format: float]")
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130 parser.add_option("-d", "--default", dest="default", action="store", default=None, type="float", help="value if tag is not present [format: float]")
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131 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
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132 parser.add_option("-y", "--mysql", dest="mysql", action="store_true", default=False, help="write output into MySQL tables [format: boolean] [default: False]")
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133 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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134 (options, args) = parser.parse_args()
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135
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136 selectByTag = SelectByTag(options.verbosity)
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137 selectByTag.input = options.inputFileName
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138 selectByTag.format = options.format
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139 selectByTag.tag = options.tag
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140 selectByTag.value = options.value
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141 selectByTag.min = options.min
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142 selectByTag.max = options.max
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143 selectByTag.default = options.default
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144 selectByTag.output = options.outputFileName
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145 selectByTag.mysql = options.mysql
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146 selectByTag.run()
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147
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148
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