Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/parsing/SsrParser.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed 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)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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=''):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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