本文整理汇总了Python中Helper.Helper.proceedCommand方法的典型用法代码示例。如果您正苦于以下问题：Python Helper.proceedCommand方法的具体用法？Python Helper.proceedCommand怎么用？Python Helper.proceedCommand使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Helper.Helper的用法示例。
在下文中一共展示了Helper.proceedCommand方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: startAnalysis
# 需要导入模块: from Helper import Helper [as 别名]
# 或者: from Helper.Helper import proceedCommand [as 别名]
def startAnalysis(self):
recaledBamFile=self.rnaEdit.params.output+".noDup.realigned.recalibrated.bam"
if os.path.isfile(recaledBamFile):
Helper.info("* * * [Skipping] Mapping result File already exists * * *",self.rnaEdit.logFile,self.rnaEdit.textField)
self.rnaEdit.logFile.flush()
return recaledBamFile
if self.rnaEdit.params.paired == True: #For paired end sequencing
#Align first Fastq Reads to the Genome
saiFile1=self.rnaEdit.params.output+"_1.sai"
cmd = [self.rnaEdit.params.sourceDir+"bwa", "aln" , "-t",self.rnaEdit.params.threads, "-n", self.rnaEdit.params.maxDiff , "-k", self.rnaEdit.params.seedDiff, self.rnaEdit.params.refGenome, self.fastqFile1]
Helper.proceedCommand("Align first Reads with BWA", cmd, self.fastqFile1, saiFile1, self.rnaEdit)
#Align second Fastq Reads to the Genome
saiFile2=self.rnaEdit.params.output+"_2.sai"
cmd = [self.rnaEdit.params.sourceDir+"bwa", "aln" , "-t",self.rnaEdit.params.threads, "-n", self.rnaEdit.params.maxDiff , "-k", self.rnaEdit.params.seedDiff, self.rnaEdit.params.refGenome, self.fastqFile2]
Helper.proceedCommand("Align second Reads with BWA", cmd, self.fastqFile2, saiFile2, self.rnaEdit)
#convert sai to sam
samFile=self.rnaEdit.params.output+".sam"
cmd = [self.rnaEdit.params.sourceDir + "bwa", "sampe", "-r", "@RG\tID:bwa\tSM:A\tPL:ILLUMINA\tPU:HiSEQ2000", self.rnaEdit.params.refGenome, saiFile1, saiFile2, self.fastqFile1, self.fastqFile2]
Helper.proceedCommand("convert sai to sam", cmd, saiFile1, samFile, self.rnaEdit)
elif self.rnaEdit.params.paired == False: #For single end sequencing
#Align Fastq Reads to the Genome
saiFile=self.rnaEdit.params.output+".sai"
cmd = [self.rnaEdit.params.sourceDir+"bwa", "aln" , "-t",self.rnaEdit.params.threads, "-n", self.rnaEdit.params.maxDiff , "-k", self.rnaEdit.params.seedDiff, self.rnaEdit.params.refGenome, self.fastqFile]
Helper.proceedCommand("Align Reads with BWA", cmd, self.fastqFile, saiFile, self.rnaEdit)
#convert sai to sam
samFile=self.rnaEdit.params.output+".sam"
cmd = [self.rnaEdit.params.sourceDir + "bwa", "samse", "-r", "@RG\tID:bwa\tSM:A\tPL:ILLUMINA\tPU:HiSEQ2000", self.rnaEdit.params.refGenome, saiFile, self.fastqFile]
#cmd = [self.rnaEdit.params.sourceDir + "bwa", "samse", self.rnaEdit.params.refGenome, saiFile, self.fastqFile]
Helper.proceedCommand("convert sai to sam", cmd, saiFile, samFile, self.rnaEdit)
#convert sam to bam
unsortedBamFile=self.rnaEdit.params.output+".unsorted.bam"
bamFile=self.rnaEdit.params.output+".bam"
"""
cmd=["java", "-Xmx8
G", "-jar", self.rnaEdit.params.sourceDir + "picard-tools/SortSam.jar", "INPUT=" + samFile, "OUTPUT=" + bamFile, "SO=coordinate", "VALIDATION_STRINGENCY=LENIENT", "CREATE_INDEX=true"]
Helper.proceedCommand("convert sam to bam", cmd, samFile, bamFile, self.rnaEdit)
"""
#Sort and Index Bam File
#Helper.status("Sort Bam", self.rnaEdit.logFile,self.rnaEdit.textField)
'''pysamSamFile = pysam.Samfile(samFile,'r')
pysamBamFile = pysam.Samfile(unsortedBamFile,'wb', template=pysamSamFile)
for read in pysamSamFile.fetch():
pysamBamFile.write(read)'''
#pysam.sort(samFile,"-o", bamFile)
cmd = [self.rnaEdit.params.sourceDir + "samtools", "sort", samFile,"-o", bamFile]
Helper.proceedCommand("Sort Bam File", cmd, samFile, bamFile, self.rnaEdit)
#Helper.status("index Bam", self.rnaEdit.logFile,self.rnaEdit.textField)
#pysam.index(bamFile)
cmd = [self.rnaEdit.params.sourceDir + "samtools", "index", bamFile]
Helper.proceedCommand("Index Bam File", cmd, samFile, bamFile+".bai", self.rnaEdit)
#mark PCR duplicates
#Helper.status("Remove Duplicates", self.rnaEdit.logFile,self.rnaEdit.textField)
markedFile=self.rnaEdit.params.output+".noDup.bam"
cmd=["java","-Xmx16G","-jar",self.rnaEdit.params.sourceDir + "picard-tools/MarkDuplicates.jar","INPUT=" + bamFile, "OUTPUT=" + markedFile, "METRICS_FILE="+self.rnaEdit.params.output+".pcr.metrics", "VALIDATION_STRINGENCY=LENIENT", "CREATE_INDEX=true"]
Helper.proceedCommand("Remove PCR duplicates", cmd, bamFile, markedFile, self.rnaEdit)
"""if self.rnaEdit.params.paired == False:
pysam.rmdup("-s",bamFile,markedFile)
else:
pysam.rmdup(bamFile,markedFile)
#pysam.rmdup(bamFile,markedFile)
if self.rnaEdit.params.paired == False:
cmd = [self.rnaEdit.params.sourceDir + "samtools", "rmdup", "-s", bamFile, markedFile]
else:
cmd = [self.rnaEdit.params.sourceDir + "samtools", "rmdup", bamFile, markedFile]
Helper.proceedCommand("Index Bam File", cmd, bamFile, markedFile, self.rnaEdit)
Helper.status("index Bam", self.rnaEdit.logFile,self.rnaEdit.textField)
pysam.index(markedFile)
cmd = [self.rnaEdit.params.sourceDir + "samtools", "index", bamFile]
Helper.proceedCommand("Index Bam File", cmd, bamFile, markedFile+".bai", self.rnaEdit)
#return bamFile"""
#run Alignement with tophat
"""
bamFile=self.rnaEdit.params.output+"/accepted_hits.bam"
cmd=[self.rnaEdit.params.sourceDir + "tophat/tophat2", "--no-coverage-search","--keep-fasta-order", "-p", "12", "--rg-id", "A","--rg-sample","A","--rg-library","illumina","--rg-platform-unit","HiSeq", "-o", self.rnaEdit.params.output, self.rnaEdit.params.refGenome, self.fastqFile ]
print cmd
Helper.proceedCommand("Map reads with tophat", cmd, self.rnaEdit.params.fastqFile, bamFile, self.rnaEdit.)
"""
#.........这里部分代码省略.........