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1 #!/usr/bin/env python
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2
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3 # Copyright INRA (Institut National de la Recherche Agronomique)
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4 # http://www.inra.fr
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5 # http://urgi.versailles.inra.fr
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6 #
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7 # This software is governed by the CeCILL license under French law and
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8 # abiding by the rules of distribution of free software. You can use,
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9 # modify and/ or redistribute the software under the terms of the CeCILL
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10 # license as circulated by CEA, CNRS and INRIA at the following URL
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11 # "http://www.cecill.info".
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12 #
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13 # As a counterpart to the access to the source code and rights to copy,
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14 # modify and redistribute granted by the license, users are provided only
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15 # with a limited warranty and the software's author, the holder of the
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16 # economic rights, and the successive licensors have only limited
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17 # liability.
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18 #
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19 # In this respect, the user's attention is drawn to the risks associated
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20 # with loading, using, modifying and/or developing or reproducing the
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21 # software by the user in light of its specific status of free software,
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22 # that may mean that it is complicated to manipulate, and that also
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23 # therefore means that it is reserved for developers and experienced
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24 # professionals having in-depth computer knowledge. Users are therefore
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25 # encouraged to load and test the software's suitability as regards their
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26 # requirements in conditions enabling the security of their systems and/or
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27 # data to be ensured and, more generally, to use and operate it in the
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28 # same conditions as regards security.
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29 #
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30 # The fact that you are presently reading this means that you have had
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31 # knowledge of the CeCILL license and that you accept its terms.
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32
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33
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34 import os
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35 import sys
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36 import ConfigParser
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37
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38 from commons.core.sql.DbMySql import DbMySql
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39 from commons.core.utils.RepetOptionParser import RepetOptionParser
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40 from commons.core.utils.FileUtils import FileUtils
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41 from commons.core.parsing.FastaParser import FastaParser
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42 from ConfigParser import MissingSectionHeaderError
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43 from commons.core.sql.DbFactory import DbFactory
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44 from commons.core.sql.TablePathAdaptator import TablePathAdaptator
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45 from commons.core.LoggerFactory import LoggerFactory
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46
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47 #TODO: use configuration file
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48
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49 LOG_DEPTH = "repet.tools"
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50
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51 ## Get 3 annotation files, using output from TEannot:
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52 #- consensus with one or more full length copy,
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53 #- consensus with one or more full length fragment,
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54 #- consensus without copy
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55
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56 class SplicerFromAnnotation(object):
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57
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58 def __init__(self, inInfoFileName = "", tableName = "", verbose = 0):
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59 self._inInfoFileName = inInfoFileName
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60 self._tableName = tableName
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61 self._verbosity = verbose
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62 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
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63
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64 def _logAndRaise(self, errorMsg):
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65 self._log.error(errorMsg)
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66 raise Exception(errorMsg)
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67
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68 def setAttributesFromCmdLine(self):
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69 desc = "Splice annotations from genome. These annotations are Full Length Copy or Full Length Fragment according to consensus."
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70 desc += "A TEs library and annotation are necessary. Connection to the database parameters are retrieved from the environment"
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71
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72 examples = "\nExample : with a project called \"MyTEannotAnalysis\":\n"
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73 examples += "\t$ python SplicerFromAnnotation.py -i inputFastaFileName -C configFileName -t MyTEannotAnalysis_refTEs_seq "
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74 examples += "\n\t"
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75 examples += "\n\n"
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76
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77 parser = RepetOptionParser(description = desc, epilog = examples)
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78 parser.add_option("-i", "--file", dest = "inputFastaFileName", action = "store", type = "string", help = "input file (mandatory) = output file with .splice)")
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79 parser.add_option("-C", "--config", dest = "configFileName", action = "store", type = "string", help = "config file name to set database connection", default = "")
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80 parser.add_option("-t", "--copyType", dest = "copyType" , action = "store", type = "int", help = "type number [default: 1, 2] 1 is Full Length Copy", default = 1 )
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81 parser.add_option("-I", "--identity", dest = "identity", action= "store", type = "float", help = "identity between 0 and 100 [default: 80]", default = 80)
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82 parser.add_option("-o", "--outputFile",dest = "outputFile", action= "store", type = "string", help = "output fasta file (default=input File + '.splice')", default = "")
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83 parser.add_option("-v", "--verbose", dest = "verbose", action = "store", type = "int", help = "verbosity level (default=0)", default = 0)
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84 (options, args) = parser.parse_args()
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85 self._setAttributesFromOptions(options)
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86
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87 def _setAttributesFromOptions(self, options):
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88 self.setConfigFileName(options.configFileName)
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89 self.setInputFileName(options.inputFastaFileName)
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90 self.setOutputFileName(options.outputFile)
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91 self.setIdentity(options.identity)
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92 self.setCopyType(options.copyType)
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93 self.setVerbose(options.verbose)
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94
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95 def setCopyType(self, copyType):
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96 self._copyType = copyType
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97
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98 def setIdentity(self,identity):
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99 self._identity=identity
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100
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101 def setInputFileName(self, inputFastaFileName):
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102 self._inputFastaFileName = inputFastaFileName
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103 self._projectName= os.path.basename(self._inputFastaFileName)
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104 self._projectName = self._projectName.split('.')[0]
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105 self._fF=FastaParser(self._inputFastaFileName)
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106 self._fF.getInfos()
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107 self.genomeSize=self._fF.size
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108 self.nbSeqGenome=self._fF.nbSequences
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109
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110 def setOutputFileName(self,outputFile):
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111 self._outputFileName = outputFile
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112
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113 def setConfigFileName(self, configFileName):
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114 self._configFileName = configFileName
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115 configFileHandle = open(self._configFileName)
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116 config = ConfigParser.ConfigParser()
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117
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118 try :
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119 config.readfp( configFileHandle )
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120 except MissingSectionHeaderError:
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121 self._logAndRaise("Config file " + self._configFileName + " must begin with a section header ")
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122
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123 self.setup_env( config )
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124
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125 def setVerbose(self, verbose):
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126 self._verbosity = verbose
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127
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128 def setup_env(self, config):
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129 os.environ["REPET_HOST"] = config.get("repet_env", "repet_host")
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130 os.environ["REPET_USER"] = config.get("repet_env", "repet_user")
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131 os.environ["REPET_PW"] = config.get("repet_env", "repet_pw")
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132 os.environ["REPET_DB"] = config.get("repet_env", "repet_db")
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133 os.environ["REPET_PORT"] = config.get("repet_env", "repet_port")
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134 os.environ["REPET_JOB_MANAGER"] = config.get("repet_env", "repet_job_manager")
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135
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136 def checkOptions(self):
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137 if self._inputFastaFileName != "":
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138 if not FileUtils.isRessourceExists(self._inputFastaFileName):
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139 self._logAndRaise("Input fasta file does not exist!")
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140 else:
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141 self._logAndRaise("No specified -i option! It is mandatory")
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142
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143 if self._outputFileName =="":
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144 self._outputFileName = os.path.basename(self._inputFastaFileName)+'.splice'
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145
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146 if self._copyType!=1 or self._copyType!=2:
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147 self._logAndRaise("Copy type must be only 1 or 2!")
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148 if self._configFileName != "":
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149 iDb = DbMySql(cfgFileName = self._configFileName)
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150 iDb.close()
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151 else:
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152 self._logAndRaise("No specified config file name!")
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153
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154
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155 def run(self):
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156 LoggerFactory.setLevel(self._log, self._verbosity)
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157 self.checkOptions()
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158
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159 msg = "START SplicerFromAnnotation"
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160 msg += "\n input info file: %s" % self._inputFastaFileName
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161 msg += "\n Copy type is: %s" % self._copyType
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162 msg += "\n identity is: %s" % self._identity
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163 msg += "\n host is: %s" % os.environ["REPET_HOST"]
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164 msg += "\n user is: %s" % os.environ["REPET_USER"]
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165 msg += "\n DB is: %s" % os.environ["REPET_DB"]
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166 msg += "\n port is: %s" % os.environ["REPET_PORT"]
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167 self._log.debug("%s\n" % msg)
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168
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169 cmd="PostAnalyzeTELib.py -a 3 -p %s_chr_allTEs_nr_noSSR_join_path -s %s_refTEs_seq -g %s" % (self._projectName,self._projectName,self.genomeSize)
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170 os.system(cmd)
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171
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172 cmd="GetSpecificTELibAccordingToAnnotation.py -i %s_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE.tab -t %s_refTEs_seq -v 2" % (self._projectName,self._projectName)
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173 os.system(cmd)
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174
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175 if self._copyType == 1 :
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176 f = open("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthCopy.txt", "r")
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177 else :
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178 f = open("Splicer_inputFile_chr_allTEs_nr_noSSR_join_path.annotStatsPerTE_FullLengthFrag.txt", "r")
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179
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180 lines=f.readlines()[1:]
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181 if len(lines)>0:
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182 lConsensusHeader_copyType=[i.split('\t',1)[0] for i in lines]
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183 db = DbFactory.createInstance()
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184
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185 sql_cmd = "CREATE TABLE %s_annotationIdentitySup%d_path SELECT * FROM %s_chr_allTEs_nr_noSSR_join_path where identity >=%f" % ( self._projectName,int(self._identity),self._projectName,self._identity)
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186 db.execute( sql_cmd )
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187
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188 iTPA = TablePathAdaptator(db, "%s_annotationIdentitySup%d_path" % (self._projectName, int(self._identity)))
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189 lAllDistinctPath=[]
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190 for consensusName in lConsensusHeader_copyType:
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191 lDistinctPath = iTPA.getIdListFromSubject(consensusName)
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192 lAllDistinctPath=lAllDistinctPath+lDistinctPath
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193
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194 iTPA = TablePathAdaptator(db,"%s_chr_allTEs_nr_noSSR_join_path" % self._projectName)
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195 sql_cmd = "CREATE TABLE %s_annotationToSplice_path LIKE %s_chr_allTEs_nr_noSSR_join_path" % ( self._projectName, self._projectName )
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196 db.execute( sql_cmd )
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197
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198 for pathId in lAllDistinctPath:
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199 sql_cmd = "INSERT INTO %s_annotationToSplice_path SELECT * FROM %s_chr_allTEs_nr_noSSR_join_path where path =%d" % ( self._projectName, self._projectName, pathId )
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200 db.execute( sql_cmd )
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201 db.close()
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202
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203 cmd="SpliceTEsFromGenome.py -i %s_annotationToSplice_path -f path -g %s -o %s -C %s -v 2" % (self._projectName, self._inputFastaFileName, self._outputFileName, self._configFileName)
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204 os.system(cmd)
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205
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206 else :
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207 msg = "There is no consensus in this copy type.\n"
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208 self._log.info(msg)
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209 f.close()
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210
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211 self._log.info("END SplicerFromAnnotation")
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212 return 0
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213
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214 if __name__ == '__main__':
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215 iGetTELib = SplicerFromAnnotation()
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216 iGetTELib.setAttributesFromCmdLine()
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217 iGetTELib.run()
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218 |
