def startProcess(readFileList,AnnotationDir,ReadLen,readType,annotation_type):
seq_depth=0
#Sample = ['Brain','UHR']
Sample = ['workfloder']
rep=readFileList
lanFile=[]
for i in range(len(readFileList)):
lanFile.append('Lane'+str(i+1))
#Create Run path function
targetDir = AnnotationDir
workfloder = os.path.join(targetDir,'workfloder')
####Annocation Files Path
GeneExonSplit = os.path.join(workfloder,'NLDMseq.Exon.Split')
GeneFile = os.path.join(workfloder,'NLDMseq.Gene.Info')
#####workfloder path
geneMapout = os.path.join(workfloder,'ModelMultiGene_Map')
geneExonout = os.path.join(workfloder,'GeneExonFile')
GeneData_Path = os.path.join(workfloder,'ExtractMultiGeneData')
GeneAbsLoc_path = os.path.join(workfloder,'ModelMultiGene_AbsLoc')
exonLen = os.path.join(workfloder,'exonLen')
exonjunfile = os.path.join(workfloder,'GeneExonFile')
spandExonsLen = os.path.join(workfloder,'exonLen')
static_exonJunc.staticGeneNewExon(GeneExonSplit,geneMapout,geneExonout)
getIsoLength.getIsoLen(GeneFile,GeneExonSplit,targetDir)#get isoform length
geneExonLen.staticGeneNewExon(GeneExonSplit,exonjunfile,spandExonsLen,ReadLen)
plusGeneName.plusGeneName(GeneFile,readFileList,targetDir,readType,annotation_type)#covert bowtie
DictIsofGene = {}
gene_list=[]
isoNo_list=[]
length_list=[]
isoName_list=[]
f = open(GeneFile,'r')
for line in f:
line = line.rstrip()
line = line.split('\t')
gene = line[0]
IsoNo = int(line[1])
IsoNameList= line[3:]
for i in xrange(IsoNo):
DictIsofGene[IsoNameList[i]]=gene
gene_list.append(line[0])
isoNo_list.append(int(line[1]))
length_list.append(int(line[2]))
isoName_list.append(line[3:])
f.close()
###########CalculateProbability and ExtractGeneData
for i in range(len(Sample)):
for j in range(len(rep)):
InputPath = os.path.join(workfloder,'readInput')
InputFile = os.path.join(InputPath,'Lane'+str(i)+'.plusGene')
FileLabel = os.path.join(workfloder,'NLDMseq.Gene.Label.Isoform')
OutputFile= os.path.join(InputPath,'Lane'+str(i))
seq_depth=Extract_BowtieData.CalculateProbability(InputFile,OutputFile,readType)
InputFile = OutputFile
OutputPath= os.path.join(GeneData_Path,lanFile[j])
Extract_BowtieData.ExtractGeneData(InputFile,OutputPath,GeneFile,FileLabel,readType)
##################CalculateAbsoluteLocation
for l in range(len(rep)):
CalLocFileInPath = os.path.join(GeneData_Path,lanFile[l])
CalLocFileOutPath = os.path.join(GeneAbsLoc_path,lanFile[l])
Extract_CalcAbsLoc.CalculateAbsoluteLocation(GeneFile,GeneExonSplit,CalLocFileInPath,CalLocFileOutPath,readType,ReadLen)
targetDir=AnnotationDir
LocInputPath = os.path.join(targetDir,'workfloder','ModelMultiGene_AbsLoc')
exonInputFile = os.path.join(targetDir,'workfloder','GeneExonFile')
exonLenFile = os.path.join(targetDir,'workfloder','exonLen')
DataOutputPath = os.path.join(targetDir,'workfloder','ModelMultiGene_Data')
NormDataOutput = os.path.join(targetDir,'workfloder','ModelMultiGene_NormData')
#function pp_work parament list and short name:
# sub_gene_list ----->sgl
# sub_length_list ----->sll
# sub_isoNo_list ----->siNol
# sub_isoName_list ----->siNamel
# LocInputFile ----->LocIF
# exonInputFile ----->exonInF
# exonLenFile ----->exonLenF
# DataOutputPath ----->DOPath
# NormDataOutput ----->NDOut
def pp_work(sgl,sll,siNol,siNamel,LocIF,exonInF,exonLenF,DOPath,NDOut):
for i in range(len(sgl)):
gene=sgl[i];
length=sll[i];
isoNo=siNol[i];
isoName=siNamel[i];
static_readOnExon.ModelMultiGeneDataScale(gene,length,isoNo,isoName,LocIF,exonInF, \
exonLenF,DOPath,NDOut);
for i in range(len(Sample)):
for j in range(len(rep)):
LocInputFile = os.path.join(LocInputPath,lanFile[j])
block_size=5000
start=0
end=len(gene_list)
job_server = pp.Server()
job_server.get_ncpus()
jobs=[]
endi=0;
starti=0;
while endi<end:
endt=starti+block_size;
endi=min(endt,end);
jobs.append(job_server.submit(pp_work,(gene_list[starti:endi], \
length_list[starti:endi],\
isoNo_list[starti:endi],\
isoName_list[starti:endi],\
LocInputFile,\
exonInputFile,\
exonLenFile,\
DataOutputPath,\
NormDataOutput),\
globals=globals()))
starti=starti+block_size;
for job in jobs:
job()
job_server.destroy()
return (seq_depth)
def startProcess(readFileList, annotation_type, AnnotationDir, ReadLen,
readType):
rep = readFileList
lanFile = []
CatFile = [
'ExtractMultiGeneData', 'ModelMultiGene_AbsLoc', 'ModelMultiGene_Data',
'ModelMultiGene_NormData'
]
for i in range(len(readFileList)):
lanFile.append('Lane' + str(i + 1))
targetDir = AnnotationDir
workfloder = os.path.join(targetDir, 'workfloder')
annotationPath = os.path.join(targetDir, 'Annotation')
####Annocation Files Path
GeneExonSplit = os.path.join(annotationPath,
annotation_type + '.Exon.Split')
GeneFile = os.path.join(annotationPath, annotation_type + '.Gene.Info')
#####workfloder path
geneMapout = os.path.join(workfloder, 'ModelMultiGene_Map')
geneExonout = os.path.join(workfloder, 'GeneExonFile')
GeneData_Path = os.path.join(workfloder, 'ExtractMultiGeneData')
GeneAbsLoc_path = os.path.join(workfloder, 'ModelMultiGene_AbsLoc')
exonLen = os.path.join(workfloder, 'exonLen')
exonjunfile = os.path.join(workfloder, 'GeneExonFile')
spandExonsLen = os.path.join(workfloder, 'exonLen')
readNumFile = os.path.join(workfloder, 'seq_depth')
static_exonJunc.staticGeneNewExon(GeneExonSplit, geneMapout, geneExonout)
getIsonum.getIsonum(GeneExonSplit, targetDir)
getIsoLength.getIsoLen(GeneFile, GeneExonSplit,
targetDir) #get isoform length
geneExonLen.staticGeneNewExon(GeneExonSplit, exonjunfile, spandExonsLen,
ReadLen)
plusGeneName.plusGeneName(GeneFile, readFileList, targetDir, readType,
ReadLen) #covert bowtie
DictIsofGene = {}
gene_list = []
isoNo_list = []
length_list = []
isoName_list = []
f = open(GeneFile, 'r')
for line in f:
line = line.rstrip()
line = line.split('\t')
gene = line[0]
IsoNo = int(line[1])
IsoNameList = line[3:]
for i in xrange(IsoNo):
DictIsofGene[IsoNameList[i]] = gene
gene_list.append(line[0])
isoNo_list.append(int(line[1]))
length_list.append(int(line[2]))
isoName_list.append(line[3:])
f.close()
targetDir = AnnotationDir
LocInputPath = os.path.join(targetDir, 'workfloder',
'ModelMultiGene_AbsLoc')
exonInputFile = os.path.join(targetDir, 'workfloder', 'GeneExonFile')
exonLenFile = os.path.join(targetDir, 'workfloder', 'exonLen')
DataOutputPath = os.path.join(targetDir, 'workfloder',
'ModelMultiGene_Data')
NormDataOutput = os.path.join(targetDir, 'workfloder',
'ModelMultiGene_NormData')
if readType == 'Paired':
for j in range(len(rep)):
InputPath = os.path.join(workfloder, 'readInput')
InputFile = os.path.join(InputPath, 'Lane' + str(j) + '.plusGene')
OutputFile = os.path.join(GeneData_Path, lanFile[j])
print InputFile
print OutputFile
PE_Extract_BowtieData.ExtractGeneBowtieData(
InputFile, GeneFile, OutputFile, readNumFile)
for l in range(len(rep)):
CalLocFileInPath = os.path.join(GeneData_Path, lanFile[l])
CalLocFileOutPath = os.path.join(GeneAbsLoc_path, lanFile[l])
print CalLocFileInPath
print CalLocFileOutPath
PE_Extract_CalcAbsLoc_my.CalculateAbsoluteLocation(
GeneFile, GeneExonSplit, CalLocFileInPath, CalLocFileOutPath,
ReadLen)
if readType == 'Single':
for j in range(len(rep)):
InputPath = os.path.join(workfloder, 'readInput')
InputFile = os.path.join(InputPath, 'Lane' + str(j) + '.plusGene')
OutputFile = os.path.join(GeneData_Path, lanFile[j])
print InputFile
print OutputFile
SE_Extract_BowtieData.ExtractGeneBowtieData(
InputFile, GeneFile, OutputFile, readNumFile)
for l in range(len(rep)):
CalLocFileInPath = os.path.join(GeneData_Path, lanFile[l])
CalLocFileOutPath = os.path.join(GeneAbsLoc_path, lanFile[l])
print CalLocFileInPath
print CalLocFileOutPath
SE_Extract_CalcAbsLoc_my.CalculateAbsoluteLocation(
GeneFile, GeneExonSplit, CalLocFileInPath, CalLocFileOutPath,
ReadLen)
f_in = open(GeneFile, 'r')
for line in f_in:
line = line.rstrip()
line = line.split('\t')
gene = line[0]
isoNo = int(line[1])
length = int(line[2])
isoName = line[3:]
for j in range(len(rep)):
LocInputPath = os.path.join(targetDir, 'workfloder')
LocInputFile = os.path.join(LocInputPath, CatFile[1])
LocInputFile = os.path.join(LocInputFile, lanFile[j])
exonInputFile = os.path.join(targetDir, 'workfloder')
exonInputFile = os.path.join(exonInputFile, 'GeneExonFile')
exonLenFile = os.path.join(targetDir, 'workfloder')
exonLenFile = os.path.join(exonLenFile, 'exonLen')
DataOutputPath = os.path.join(targetDir, 'workfloder')
DataOutputFile = os.path.join(DataOutputPath, CatFile[2])
NormDataOutput = os.path.join(DataOutputPath, CatFile[3])
static_readOnExon.ModelMultiGeneDataScale(
j, gene, length, isoNo, isoName, LocInputFile, exonInputFile,
exonLenFile, DataOutputFile, NormDataOutput)
f_in.close()
if not os.path.exists(mapFile): os.mkdir(mapFile) GeneExonFile=os.path.join(targetDir,'workfloder') GeneExonFile=os.path.join(GeneExonFile,'GeneExonFile') if not os.path.exists(GeneExonFile): os.mkdir(GeneExonFile) geneMapout=mapFile geneExonout=GeneExonFile get_map.mapout(TargetGeneExonSplitFile,geneMapout,geneExonout)#get isoform Map getIsoLength.getIsoLen(TargetGeneFile,TargetGeneExonSplitFile)#get isoform length exonLen=os.path.join(targetDir,'workfloder') exonLen=os.path.join(exonLen,'exonLen') if not os.path.exists(exonLen): os.mkdir(exonLen) ReadLen=100 exonjunfile=os.path.join(targetDir,'workfloder') exonjunfile=os.path.join(exonjunfile,'GeneExonFile') spandExonsLen=os.path.join(targetDir,'workfloder') spandExonsLen=os.path.join(spandExonsLen,'exonLen') SE_geneExonLen.staticGeneNewExon(TargetGeneExonSplitFile,spandExonsLen)
