Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/SsrParser.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 # Copyright INRA (Institut National de la Recherche Agronomique) |
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2 # http://www.inra.fr |
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3 # http://urgi.versailles.inra.fr |
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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 import sys |
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32 |
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33 ## this class can parse a Ssr results output file. SSR.pl is developped by S.Cartinhour. (5/2000) |
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34 # |
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35 class SsrParser(object): |
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36 |
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37 |
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38 def __init__(self, BES_name='', BES_redundancy='', SSR_nbNucleotides='', SSR_Motif='', SSR_Motif_number='', SSR_start='', SSR_end='', BES_size=''): |
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39 self._BesName = BES_name |
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40 self._BesRedundancy = BES_redundancy |
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41 self._SsrNbNucleotides = SSR_nbNucleotides |
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42 self._SsrMotif = SSR_Motif |
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43 self._SsrMotifNumber = SSR_Motif_number |
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44 self._SsrStart = SSR_start |
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45 self._SsrEnd = SSR_end |
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46 self._BesSize = BES_size |
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47 |
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48 def __eq__(self, o): |
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49 return self._BesName == o._BesName and self._BesRedundancy == o._BesRedundancy and self._SsrNbNucleotides == o._SsrNbNucleotides and self._SsrMotif == o._SsrMotif and self._SsrMotifNumber == o._SsrMotifNumber and self._SsrStart == o._SsrStart and self._SsrEnd == o._SsrEnd and self._BesSize == o._BesSize |
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50 |
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51 def setBesName(self, BES_Name): |
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52 self._BesName = BES_Name |
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53 |
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54 def setBesRedundancy(self, BES_redundancy): |
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55 self._BesRedundancy = BES_redundancy |
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56 |
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57 def setSsrNbNucleotides(self, SSR_nbNucleotides): |
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58 self._SsrNbNucleotides = SSR_nbNucleotides |
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59 |
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60 def setSsrMotif(self, SSR_Motif): |
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61 self._SsrMotif = SSR_Motif |
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62 |
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63 def setSsrMotifNumber(self, SSR_Motif_number): |
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64 self._SsrMotifNumber = SSR_Motif_number |
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65 |
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66 def setSsrStart(self, SSR_start): |
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67 self._SsrStart = SSR_start |
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68 |
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69 def setSsrEnd(self, SSR_end): |
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70 self._SsrEnd = SSR_end |
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71 |
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72 def setBesSize(self, BES_size): |
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73 self._BesSize = BES_size |
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74 |
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75 def getBesName(self): |
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76 return self._BesName |
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77 |
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78 def getBesRedundancy(self): |
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79 return self._BesRedundancy |
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80 |
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81 def getSsrNbNucleotides(self): |
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82 return self._SsrNbNucleotides |
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83 |
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84 def getSsrMotif(self): |
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85 return self._SsrMotif |
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86 |
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87 def getSsrMotifNumber(self): |
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88 return self._SsrMotifNumber |
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89 |
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90 def getSsrStart(self): |
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91 return self._SsrStart |
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92 |
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93 def getSsrEnd(self): |
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94 return self._SsrEnd |
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95 |
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96 def getBesSize(self): |
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97 return self._BesSize |
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98 |
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99 def setAttributes(self, lResults, iCurrentLineNumber): |
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100 error = False |
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101 |
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102 if lResults[0] != '': |
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103 self.setBesName(lResults[0]) |
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104 else: |
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105 sys.stderr.write("WARNING: The field BES Name is empty in SSR results file in line %s\n" % iCurrentLineNumber) |
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106 error = True |
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107 |
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108 if lResults[1] != '': |
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109 self.setBesRedundancy(lResults[1]) |
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110 else: |
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111 sys.stderr.write("WARNING: The field BES Redundancy is empty in SSR results file in line %s\n" % iCurrentLineNumber) |
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112 error = True |
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113 |
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114 if lResults[2] != '': |
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115 self.setSsrNbNucleotides(lResults[2]) |
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116 else: |
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117 sys.stderr.write("WARNING: The field SSR Number Nucleotides is empty in SSR results file in line %s\n" % iCurrentLineNumber) |
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118 error = True |
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119 |
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120 if lResults[3] != '': |
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121 self.setSsrMotif(lResults[3]) |
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122 else: |
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123 sys.stderr.write("WARNING: The field SSR Motif is empty in SSR results file in line %s\n" % iCurrentLineNumber) |
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124 error = True |
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125 |
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126 if lResults[4] != '': |
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127 self.setSsrMotifNumber(lResults[4]) |
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128 else: |
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129 sys.stderr.write("WARNING: The field SSR Motif Number is empty in SSR results file in line %s\n" % iCurrentLineNumber) |
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130 error = True |
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131 |
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132 if lResults[5] != '': |
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133 self.setSsrStart(lResults[5]) |
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134 else: |
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135 sys.stderr.write("WARNING: The field SSR Start is empty in SSR results file in line %s\n" % iCurrentLineNumber) |
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136 error = True |
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137 |
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138 if lResults[6] != '': |
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139 self.setSsrEnd(lResults[6]) |
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140 else: |
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141 sys.stderr.write("WARNING: The field SSR End is empty in SSR results file in line %s\n" % iCurrentLineNumber) |
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142 error = True |
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143 |
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144 if lResults[7] != '': |
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145 self.setBesSize(lResults[7]) |
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146 else: |
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147 sys.stderr.write("WARNING: The field BES Size is empty in SSR results file in line %s\n" % iCurrentLineNumber) |
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148 error = True |
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149 |
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150 if error == True: |
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151 self._setAllToNull() |
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152 |
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153 def setAttributesFromString(self, ssrLine, iCurrentLineNumber ="", fieldSeparator ="\t"): |
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154 ssrLine = ssrLine.rstrip() |
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155 lSsrLineItem = ssrLine.split(fieldSeparator) |
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156 if len(lSsrLineItem) < 8: |
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157 sys.stderr.write("WARNING: The line %s is not a valid SSR Result line\n" % iCurrentLineNumber) |
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158 else: |
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159 self.setAttributes(lSsrLineItem, iCurrentLineNumber) |
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160 |
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161 def _setAllToNull(self): |
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162 self._BesName = '' |
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163 self._BesRedundancy = '' |
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164 self._SsrNbNucleotides = '' |
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165 self._SsrMotif = '' |
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166 self._SsrMotifNumber = '' |
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167 self._SsrStart = '' |
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168 self._SsrEnd = '' |
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169 self._BesSize = '' |
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170 |