Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/Java/Python/SelectByTag.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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 |