def generatePics(currentRunDir):
try:
print "generatePics"
call = "cat " + projectBinDir + "r_analyseClustering.R | R --slave --args " + currentRunDir
NGS_Util.executeCall(call)
picsDir = NGS_Util.createDirectoryPath(currentRunDir, "PicsTables")
epsFile = NGS_Util.createFilePath(picsDir, "SenSpeVsInfAll.eps")
pngFile = NGS_Util.createFilePath(picsDir, "SenSpeVsInfAll.png")
call = "convert " + epsFile + " " + pngFile
NGS_Util.executeCall(call)
except Exception:
print traceback.print_exc()
return ""
def initialize(self, orgListFile, orgFastaDir, orgBlastResDir, jointBlastDir, orgGTGBlastResDir, GTGBestHitsDir, GTGKNNDir, orgIPRScanDir, InterProScan_EC_RAW_results, moveToDir): #, new_seq_org_list):
try:
self.orgListFile = orgListFile
self.orgFastaDir = orgFastaDir
self.orgBlastResDir = orgBlastResDir
self.jointBlastDir = jointBlastDir
self.orgGTGBlastResDir = orgGTGBlastResDir
self.GTGBestHitsDir = GTGBestHitsDir
self.GTGKNNDir = GTGKNNDir
self.orgIPRScanDir = orgIPRScanDir
self.InterProScan_EC_RAW_results = InterProScan_EC_RAW_results
self.moveToDir = moveToDir
self.moveToDir_orgBlastResDir = NGS_Util.createDirectoryPath(self.moveToDir, "blast_results")
self.moveToDir_jointBlastDir = NGS_Util.createDirectoryPath(self.moveToDir, "blast_joint_results")
self.moveToDir_orgGTGBlastResDir = NGS_Util.createDirectoryPath(self.moveToDir, "GTG_blast_results")
self.moveToDir_GTGBestHitsDir = NGS_Util.createDirectoryPath(self.moveToDir, "GTG_best_hits")
self.moveToDir_GTGKNNDir = NGS_Util.createDirectoryPath(self.moveToDir, "GTG_knn")
self.moveToDir_orgIPRScanDir = NGS_Util.createDirectoryPath(self.moveToDir, "iprscan_results")
self.moveToDir_InterProScan_EC_RAW_results = NGS_Util.createDirectoryPath(self.moveToDir, "iprscan_ec_raw_results") #InterProScan_EC_RAW_results
except Exception:
print traceback.print_exc()
def splitFiles(self, organismName):
try:
print "splitFiles: " + organismName
org_fasta = NGS_Util.createFilePath(self.orgFastaDir, organismName + ".faa")
org_ipr_split_dir = NGS_Util.createDirectoryPath(self.orgIPRScanDir, organismName)
call = "sh " + ScriptsDir.IPRScanScripts_fsplit + " " + org_fasta + " " + org_ipr_split_dir
NGS_Util.executeCall(call)
return org_ipr_split_dir
except Exception:
print traceback.print_exc()
return ""
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()
############################################################################################################################################################################################################ Java_PATH = "/usr/java/latest/bin/" LibSBML_PATH = "/share/apps/local/lib64/python2.6/site-packages/" ############################################################################################################################################################################################################ fastaSplitNDir = "Path to the program to cut the fasta file in pieces called fastasplitN (Author: David Mathog, Biology Division, Caltech") fastaSplitN = NGS_Util.createFilePath(fastaSplitNDir,"fastasplitn") ############################################################################################################################################################################################### projectBinDir = NGS_Util.createDirectoryPath(projectDir,"bin") BLASTScripts = NGS_Util.createDirectoryPath(projectDir,"Blast_scripts") BlastScripts_blast=BLASTScripts + "blast.bash" BlastScripts_blastp_bwdblast=BLASTScripts + "blastp_bwdblast.bash" BlastScripts_blastp_fwdblast=BLASTScripts + "blastp_fwdblast.bash" BlastScripts_makeblastdb_AUTO=BLASTScripts + "makeblastdb_AUTO.bash" BlastScripts_makedustfile_AUTO=BLASTScripts + "makedustfile_AUTO.bash" BlastScripts_buildBlastResult=BLASTScripts + "buildBlastResult.py" BlastScripts_combineAllBlasts=BLASTScripts + "combineAllBlasts.py" BlastScripts_getEcs=BLASTScripts + "getEcs.py" BlastScripts_rectify_blastresult=BLASTScripts + "rectify_blastresult.py" GTGScripts = NGS_Util.createDirectoryPath(projectDir,"GTG_scripts") GTGScripts_reform_knn= GTGScripts + "reform_knn.py"
#!/usr/bin/env python """ Author: M. Fahad Syed ([email protected]) """ import os import sys import traceback import NGS_Util projectDir = "/etc/ProSol/" # needs to be initialized projectBinDir = NGS_Util.createDirectoryPath(projectDir, "bin") ########################################################################################## Blast Toolkit ########################################################################################## BlastDir = "/etc/Blast/ncbi-blast-2.2.28+/bin/" #Needs to be set the user# BlastDBDir = NGS_Util.createDirectoryPath(projectDir, "data/BlastDB") BlastDustDir = NGS_Util.createDirectoryPath(projectDir, "data/BlastDB") ############################################################################################################################################################################################################ pfamScanDir = "/etc/PfamScan/" ############################################################################################################################################################################################################ ProSol_Thresholding = NGS_Util.createFilePath(projectBinDir, "GetThreshold.py")
#!/usr/bin/env python """ Author: M. Fahad Syed ([email protected]) """ import sys sys.path.append("model_reconstruction_pipeline") import NGS_Util import ScriptsDir projectDir = ScriptsDir.projectDir #Needs to be set the user# projectBinDir = NGS_Util.createDirectoryPath(projectDir,"bin") projectDataDir = NGS_Util.createDirectoryPath(projectDir,"data") projectResultDir = NGS_Util.createDirectoryPath(projectDir,"results") ########################################################################################## Blast Toolkit ########################################################################################## orgBlastDBDir = ScriptsDir.BlastDBDir orgBlastDustDir = ScriptsDir.BlastDustDir ########################################################################################## Uniprot Data Files ########################################################################################## uniprot_fasta = NGS_Util.createFilePath(projectDataDir, "Uniprot_EC_GO_Data/uniprot_sprot.fasta") uniprot_sprot_dat = NGS_Util.createFilePath(projectDataDir, "Uniprot_EC_GO_Data/uniprot_sprot.dat") uniprot_dust = NGS_Util.createFilePath(orgBlastDustDir, "uniprot_dust.asnb") uniprot_blast_db = NGS_Util.createFilePath(orgBlastDBDir, "uniprot") ########################################################################################## EC Go Data Files ########################################################################################## ec_files = NGS_Util.createFilePath(projectDataDir, "Uniprot_EC_GO_Data/ec_files.txt")
#!/usr/bin/env python """ Author: M. Fahad Syed ([email protected]) """ import os import sys import traceback import datetime import ScriptsDir import NGS_Util import ProSol_PreProcess import ProSol projectDir = ScriptsDir.projectDir projectBinDir = NGS_Util.createDirectoryPath(projectDir, "bin") projectDataDir = NGS_Util.createDirectoryPath(projectDir, "data") projectResultsDir = NGS_Util.createDirectoryPath(projectDir, "results") orgListFile = NGS_Util.createFilePath(projectDataDir, "org_list.txt") orgFastaDir = NGS_Util.createDirectoryPath(projectDataDir, "Genomes_Oct2013") accession2speciesFile = NGS_Util.createFilePath(projectResultsDir, "accession2species.txt") species2accessionFile = NGS_Util.createFilePath(projectResultsDir, "species2accession.txt") interpro_xml = NGS_Util.createFilePath(projectDataDir, "interpro.xml") PfamA_hmm_file = NGS_Util.createFilePath(projectDataDir, "Pfam-A.hmm") pfamDatfile = NGS_Util.createFilePath(projectDataDir, "Pfam-A.hmm.dat") pfamDataDir = projectDataDir
########################################################################################## Blast Toolkit ########################################################################################## BlastDir = "Tools/ncbi-blast-2.2.28+/bin/" BlastDBDir = "Tools/ncbi-blast-2.2.28+/db/" #Needs to be set the user# BlastDustDir = "Tools/ncbi-blast-2.2.28+/db/" #Needs to be set the user# ########################################################################################## Blast Toolkit ########################################################################################## IprscanDir = "Tools/iprscan/bin/" ############################################################################################################################################################################################### #projectBinDir = NGS_Util.createDirectoryPath(projectDir,"bin") BLASTScripts = NGS_Util.createDirectoryPath(projectDir, "Blast_scripts") BlastScripts_blast = BLASTScripts + "blast.bash" BlastScripts_blastp_bwdblast = BLASTScripts + "blastp_bwdblast.bash" BlastScripts_blastp_fwdblast = BLASTScripts + "blastp_fwdblast.bash" BlastScripts_makeblastdb_AUTO = BLASTScripts + "makeblastdb_AUTO.bash" BlastScripts_makedustfile_AUTO = BLASTScripts + "makedustfile_AUTO.bash" BlastScripts_buildBlastResult = BLASTScripts + "buildBlastResult.py" BlastScripts_combineAllBlasts = BLASTScripts + "combineAllBlasts.py" BlastScripts_getEcs = BLASTScripts + "getEcs.py" BlastScripts_rectify_blastresult = BLASTScripts + "rectify_blastresult.py" GTGScripts = NGS_Util.createDirectoryPath(projectDir, "GTG_scripts") GTGScripts_reform_knn = GTGScripts + "reform_knn.py" GTGScripts_reform = GTGScripts + "reform.py" GTGScripts_linebuffer = GTGScripts + "linebuffer.py" GTGScripts_gtgknn = GTGScripts + "gtgknn.py"
