Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/checker/CheckerUtils.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 |
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32 import os |
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33 import sys |
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34 import re |
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35 import glob |
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36 import ConfigParser |
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37 from ConfigParser import NoOptionError |
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38 from ConfigParser import NoSectionError |
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39 from commons.core.checker.CheckerException import CheckerException |
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40 |
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41 |
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42 ## A set of static methods used to perform checks. |
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43 # |
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44 # |
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45 class CheckerUtils( object ): |
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46 |
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47 ## Check if blastName param is in ["blastn", "blastp", "blastx", "tblastn", "tblastx"] |
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48 # |
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49 # @param blastName name to check |
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50 # @return True if name is in list False otherwise |
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51 # |
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52 def isBlastNameNotInBlastValues( blastName ): |
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53 blastValuesSet = set( ["blastn", "blastp", "blastx", "tblastn", "tblastx"] ) |
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54 blastNameSet = set( [ blastName ] ) |
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55 return not blastNameSet.issubset( blastValuesSet ) |
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56 |
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57 isBlastNameNotInBlastValues = staticmethod( isBlastNameNotInBlastValues ) |
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58 |
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59 |
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60 ## Check if param is NOT "TRUE" and NOT false "FALSE" |
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61 # |
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62 # @param param str to check |
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63 # @return True if param is not eq to "TRUE" AND not eq to "FALSE", false otherwise |
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64 # |
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65 def isNotTRUEisNotFALSE( param ): |
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66 return param != "TRUE" and param != "FALSE" |
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67 |
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68 isNotTRUEisNotFALSE = staticmethod( isNotTRUEisNotFALSE ) |
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69 |
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70 |
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71 ## Check if resource (file or dir) do NOT exists |
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72 # |
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73 # @param resource file or dir to check |
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74 # @return True if resource exists False otherwise |
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75 # |
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76 def isRessourceNotExits( resource ): |
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77 return not os.path.exists( resource ) |
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78 |
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79 isRessourceNotExits = staticmethod( isRessourceNotExits ) |
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80 |
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81 |
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82 ## Check a specific E-value format: de-dd |
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83 # |
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84 # @param param E-value to check |
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85 # @return True if format is de-dd False otherwise |
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86 # |
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87 def isNotAeValueWithOneDigit2DecimalsAtLeast( param ): |
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88 # \d\d stands for 2 digits and more ??? |
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89 return not re.match( "\de\-\d\d", param ) |
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90 |
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91 isNotAeValueWithOneDigit2DecimalsAtLeast = staticmethod( isNotAeValueWithOneDigit2DecimalsAtLeast ) |
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92 |
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93 |
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94 ## Check a number format |
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95 # |
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96 # @param param value to check |
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97 # @return True if param is a number (d+) False otherwise |
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98 # |
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99 def isNotANumber( param ): |
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100 return not re.match( "\d+", param ) |
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101 |
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102 isNotANumber = staticmethod( isNotANumber ) |
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103 |
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104 |
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105 ## Check if an executable is in the user's PATH |
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106 # |
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107 # @param exeName name of the executable |
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108 # @return True if executable in user's PATH, False otherwise |
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109 # |
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110 def isExecutableInUserPath( exeName ): |
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111 dirPathList = os.environ["PATH"].split(":") |
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112 for dirPath in dirPathList: |
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113 if os.path.isdir( dirPath ): |
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114 try: |
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115 binPathList = glob.glob( dirPath + "/*" ) |
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116 except OSError, e: |
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117 continue |
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118 for binPath in binPathList: |
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119 bin = os.path.basename( binPath ) |
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120 if bin == exeName: |
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121 return True |
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122 return False |
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123 |
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124 isExecutableInUserPath = staticmethod( isExecutableInUserPath ) |
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125 |
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126 |
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127 ## Return the full path of a given executable |
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128 # |
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129 def getFullPathFromExecutable( exeName ): |
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130 lDirFromUserPath = os.environ["PATH"].split(":") |
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131 for dir in lDirFromUserPath: |
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132 if os.path.isdir( dir ): |
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133 try: |
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134 lExecutables = glob.glob( "%s/*" % ( dir ) ) |
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135 except OSError, e: |
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136 continue |
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137 for exe in lExecutables: |
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138 path, exe = os.path.split( exe ) |
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139 if exe == exeName: |
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140 return path |
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141 return "" |
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142 |
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143 getFullPathFromExecutable = staticmethod( getFullPathFromExecutable ) |
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144 |
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145 |
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146 #TODO: to remove ? |
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147 ## Check if a queue Name is valid. Warning: Only with the queue manager SGE |
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148 # |
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149 # @param fullQueueName name of the queue to test (with or without parameters) |
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150 # @return True if queue name is valid, False otherwise |
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151 # |
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152 def isQueueNameValid( fullQueueName ): |
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153 queueName = fullQueueName.split()[0] |
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154 if queueName == "none": |
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155 return True |
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156 queueFile = "queueName.txt" |
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157 if not CheckerUtils.isExecutableInUserPath( "qconf" ): |
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158 msg = "executable 'qconf' can't be found" |
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159 sys.stderr.write( "%s\n" % ( msg ) ) |
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160 return False |
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161 cmd = "qconf -sql > " + queueFile |
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162 os.system( cmd ) |
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163 queueFileHandler = open( queueFile, "r" ) |
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164 lQueueNames = queueFileHandler.readlines() |
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165 queueFileHandler.close() |
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166 os.remove( queueFile ) |
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167 queueNameValid = False |
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168 for qName in lQueueNames: |
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169 qName = qName.strip() |
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170 if qName == queueName: |
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171 queueNameValid = True |
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172 break |
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173 return queueNameValid |
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174 |
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175 isQueueNameValid = staticmethod( isQueueNameValid ) |
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176 |
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177 |
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178 ## Check if a string length is lower or equal than 15 |
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179 # |
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180 # @param strName any string |
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181 # @return True if string length is <= 15, False otherwise |
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182 # |
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183 def isMax15Char( strName ): |
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184 return (len(strName) <= 15 ) |
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185 |
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186 isMax15Char = staticmethod( isMax15Char ) |
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187 |
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188 |
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189 ## Check if a string is made with only alphanumeric or underscore character |
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190 # |
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191 # @param strName any string |
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192 # @return True if string is with alphanumeric or underscore, False otherwise |
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193 # |
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194 def isCharAlphanumOrUnderscore( strName ): |
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195 # authorized ALPHABET [a-z,A-Z,0-9,_] |
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196 p = re.compile('\W') |
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197 errList=p.findall(strName) |
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198 if len( errList ) > 0 : |
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199 return False |
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200 else: |
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201 return True |
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202 |
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203 isCharAlphanumOrUnderscore = staticmethod( isCharAlphanumOrUnderscore ) |
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204 |
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205 |
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206 ## Check if sectionName is in the configuration file |
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207 # |
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208 # @param config filehandle of configuration file |
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209 # @param sectionName string of section name to check |
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210 # @exception NoSectionError: if section not found raise a NoSectionError |
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211 # |
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212 def checkSectionInConfigFile( config, sectionName ): |
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213 if not (config.has_section(sectionName)): |
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214 raise NoSectionError(sectionName) |
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215 |
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216 checkSectionInConfigFile = staticmethod( checkSectionInConfigFile ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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217 |
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218 |
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219 ## Check if an option is in a specified section in the configuration file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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220 # |
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221 # @param config filehandle of configuration file |
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222 # @param sectionName string of section name |
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223 # @param optionName string of option name to check |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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224 # @exception NoOptionError: if option not found raise a NoOptionError |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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225 # |
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226 def checkOptionInSectionInConfigFile( config, sectionName, optionName ): |
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227 config.get( sectionName, optionName ) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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228 |
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229 checkOptionInSectionInConfigFile = staticmethod( checkOptionInSectionInConfigFile ) |
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230 |
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231 |
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232 ## Check version number coherency between configFile and CHANGELOG |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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233 # |
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234 # @param config ConfigParser Instance of configuration file |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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235 # @param changeLogFileHandle CHANGELOG file handle |
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236 # @exception NoOptionError: if option not found raise a NoOptionError |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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237 # |
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238 def checkConfigVersion( changeLogFileHandle, config ): |
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239 line = changeLogFileHandle.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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240 while not line.startswith("REPET release "): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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241 line = changeLogFileHandle.readline() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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242 numVersionChangeLog = line.split()[2] |
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243 |
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244 numVersionConfig = config.get("repet_env", "repet_version") |
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245 |
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246 if not numVersionChangeLog == numVersionConfig: |
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247 message = "*** Error: wrong config file version. Expected version num is " + numVersionChangeLog + " but actual in config file is " + numVersionConfig |
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248 raise CheckerException(message) |
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249 |
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250 checkConfigVersion = staticmethod( checkConfigVersion ) |
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251 |
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252 |
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253 ## Get version number from CHANGELOG |
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254 # |
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255 # @param changeLogFile CHANGELOG file name |
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256 # |
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257 def getVersionFromChangelogFile(changeLogFileName): |
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258 with open(changeLogFileName) as changeLogFileHandle: |
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259 line = changeLogFileHandle.readline() |
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260 while not line.startswith("REPET release "): |
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261 line = changeLogFileHandle.readline() |
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262 numVersionChangeLog = line.split()[2] |
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263 return numVersionChangeLog |
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264 |
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265 |
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266 getVersionFromChangelogFile = staticmethod( getVersionFromChangelogFile ) |
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267 |
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268 |
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269 ## Check if headers of an input file contain only alpha numeric characters and "_ : . -" |
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270 # |
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271 # @param fileHandler file handle |
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272 # @exception CheckerException if bad header raise a CheckerException |
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273 # |
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274 def checkHeaders( fileHandler ): |
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275 lHeaders = CheckerUtils._getHeaderFromFastaFile(fileHandler) |
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276 p = re.compile('[^a-zA-Z0-9_:\.\-]', re.IGNORECASE) |
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277 lWrongHeaders = [] |
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278 for header in lHeaders: |
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279 errList=p.findall(header) |
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280 if len( errList ) > 0 : |
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281 lWrongHeaders.append(header) |
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282 if lWrongHeaders != []: |
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283 exception = CheckerException() |
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284 exception.setMessages(lWrongHeaders) |
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285 raise exception |
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286 |
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287 checkHeaders = staticmethod( checkHeaders ) |
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288 |
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289 |
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290 def _getHeaderFromFastaFile( inFile ): |
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291 lHeaders = [] |
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292 while True: |
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293 line = inFile.readline() |
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294 if line == "": |
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295 break |
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296 if line[0] == ">": |
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297 lHeaders.append( line[1:-1] ) |
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298 return lHeaders |
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299 |
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300 _getHeaderFromFastaFile = staticmethod( _getHeaderFromFastaFile ) |
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301 |
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302 |
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303 ## Return True if an option is in a specified section in the configuration file, False otherwise |
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304 # |
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305 # @param config handler of configuration file |
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306 # @param sectionName string of section name |
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307 # @param optionName string of option name to check |
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308 # |
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309 def isOptionInSectionInConfig( configHandler, section, option ): |
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310 try: |
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311 CheckerUtils.checkOptionInSectionInConfigFile( configHandler, section, option ) |
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312 except NoOptionError: |
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313 return False |
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314 return True |
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315 |
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316 isOptionInSectionInConfig = staticmethod( isOptionInSectionInConfig ) |