def prepareDirectories(self, cfg):
seqDivider = pcssCluster.SeqDivider(self)
seqDivider.divideSeqsFromFasta()
cfg.setSeqDivider(seqDivider)
cfg.generateConfigFiles()
self.seqDivider = seqDivider
def dtest_preprocess(self):
configFile = "testConfig/testPcssConfig.txt"
configSpecFile = "testConfig/testConfigSpec.txt"
self.pcssConfig = configobj.ConfigObj(configFile, configspec=configSpecFile)
self.pcssConfig['fasta_file'] = os.path.join(self.pcssConfig["pcss_directory"], "data", "inputSequences", "ffSequencesFasta.txt")
self.runner = pcssTools.PcssRunner(self.pcssConfig)
self.runner.setJobDirectory(os.path.join(self.runner.pcssConfig["run_directory"], "developClusterJob"))
seqDivider = pcssCluster.SeqDivider(self.runner)
seqDivider.divideSeqsFromFasta()
seqDivider.csg.makeFullSgeScript() #needs update
def executePipeline(self):
self.updateInputFileConfig()
seqDivider = pcssCluster.SeqDivider(self)
seqDivider.mergeSvmApplicationResults()
def executePipeline(self):
seqDivider = pcssCluster.SeqDivider(self)
seqDivider.mergeSvmApplicationResults()
def executePipeline(self):
seqDivider = pcssCluster.SeqDivider(self)
seqDivider.divideSeqsFromFasta()
seqDivider.makeRunDisopredSgeScript()