preProcess.preProcess()
proSol = ProSol.ProSol()
if not redoCalculations and not resumeALLInterprosCalc:
strDate = str(datetime.date.isoformat(datetime.date.today()))
if len(runDirName) > 1:
currentRunDir = NGS_Util.createDirectoryPath(
projectResultsDir, strDate + "_" + runDirName)
else:
currentRunDir = NGS_Util.createDirectoryPath(
projectResultsDir, strDate)
NGS_Util.createDirectory(currentRunDir)
proSol.initialize(orgListFile, orgFastaDir,
accession2speciesFile, species2accessionFile,
interpro_xml, PfamA_hmm_file, blastEValue,
currentRunDir, pfamDatfile, pfamDataDir,
organismsToCompareList)
if (useALLInterpros):
proSol.runForAllInterPros()
else:
iprFile_fh = open(iprFileName)
proSol.makeOrganismsSequenceIdsDict()
taxonomy = NGS_Util.createFilePath(projectDataDir, "taxonomy") nrdb40_fasta = NGS_Util.createFilePath(projectDataDir, "GTG_database/nrdb40_v2.fasta") orgGTGDatabaseDir = NGS_Util.createDirectoryPath(projectDataDir, "GTG_database") CAA1Dir = NGS_Util.createFilePath(projectDataDir, "GTG_database/index/CAA1.index") nids_up = NGS_Util.createFilePath(projectDataDir, "GTG_database/nids.up") nrdb40_dust = NGS_Util.createFilePath(orgBlastDustDir, "nrdb40_dust.asnb") nrdb40_blast_db = NGS_Util.createFilePath(orgBlastDBDir, "nrdb40") ########################################################################################## Sequence Blast Output ###################################################################################### orgBlastResDir = NGS_Util.createDirectoryPath(projectResultDir, "blast_results") jointBlastDir = NGS_Util.createDirectoryPath(projectResultDir, "blast_joint_results") NGS_Util.createDirectory(orgBlastResDir) NGS_Util.createDirectory(jointBlastDir) ########################################################################################## Sequence GTG Output ###################################################################################### orgGTGBlastResDir = NGS_Util.createDirectoryPath(projectResultDir, "GTG_blast_results") GTGBestHitsDir = NGS_Util.createDirectoryPath(projectResultDir, "GTG_best_hits") GTGKNNDir = NGS_Util.createDirectoryPath(projectResultDir, "GTG_knn") NGS_Util.createDirectory(orgGTGBlastResDir) NGS_Util.createDirectory(GTGBestHitsDir) NGS_Util.createDirectory(GTGKNNDir) ########################################################################################## Sequence IPR Output ######################################################################################
def initialize(self, seq_org_list, jointBlastDir, GTGFungiKNNDir, fungi_InterProScan_result, phylogeneticTreeFile, modelTrainingDir):
try:
self.seq_org_list = seq_org_list
self.jointBlastDir = jointBlastDir
self.GTGFungiKNNDir = GTGFungiKNNDir
self.fungi_InterProScan_result = fungi_InterProScan_result
self.phylogeneticTreeFile = phylogeneticTreeFile
self.modelTrainingDir = modelTrainingDir
self.modelTraining_IPR_EC_Dir = NGS_Util.createDirectoryPath(self.modelTrainingDir, "IPR_EC")
self.modelTrainingBlastPVDir = NGS_Util.createDirectoryPath(self.modelTrainingDir, "BlastPValues")
self.modelTraining_EC_Scores_Dir = NGS_Util.createDirectoryPath(self.modelTrainingDir, "ECScores")
self.modelTrainingProbabilityDensityScoreDir = NGS_Util.createDirectoryPath(self.modelTrainingDir, "ProbabilityDensityScore")
self.modelTrainingTreeDir = NGS_Util.createDirectoryPath(self.modelTrainingDir, "Tree")
self.modelTrainingModelDir = NGS_Util.createDirectoryPath(self.modelTrainingDir, "Model")
NGS_Util.createDirectory(self.modelTrainingDir)
NGS_Util.createDirectory(self.modelTraining_IPR_EC_Dir)
NGS_Util.createDirectory(self.modelTrainingBlastPVDir)
NGS_Util.createDirectory(self.modelTraining_EC_Scores_Dir)
NGS_Util.createDirectory(self.modelTrainingProbabilityDensityScoreDir)
NGS_Util.createDirectory(self.modelTrainingTreeDir)
NGS_Util.createDirectory(self.modelTrainingModelDir)
if (os.path.exists(self.phylogeneticTreeFile)):
NGS_Util.copyFile( self.phylogeneticTreeFile,NGS_Util.createFilePath(self.modelTrainingTreeDir,"tree") )
self.phylogeneticTreeFile = NGS_Util.createFilePath(self.modelTrainingTreeDir,"tree")
self.treeCPDS = NGS_Util.createFilePath(self.modelTrainingTreeDir,"tree.cpds")
except Exception:
print traceback.print_exc()
