def __init__(self,bpath,npath): print "********************\n",strftime("%Y-%m-%d %H:%M:%S", gmtime()),"Start Variant calling Checking" self.bpath=bpath self.npath=npath self.name='Variantcalling' self.testcaseid=[] self.bvcfpath=PathJF.getfullname_parent(os.path.join(self.bpath,'samples'),'genome.vcf.gz','variants') self.nvcfpath=PathJF.getfullname_parent(os.path.join(self.npath,'samples'),'genome.vcf.gz','variants')
def __init__(self, bpath,npath): print "********************\n",strftime("%Y-%m-%d %H:%M:%S", gmtime()),"Start ReadFiltering" self.bpath=bpath self.npath=npath self.name='ReadFiltering' self.testcaseid=[] self.bfilterpath=PathJF.getfullname_parent(os.path.join(self.bpath,'samples'),'fastq.gz.info','filtered') self.nfilternpath=PathJF.getfullname_parent(os.path.join(self.bpath,'samples'),'fastq.gz.info','filtered')
def __init__(self, bpath,npath): print "********************\n",strftime("%Y-%m-%d %H:%M:%S", gmtime()),"Start Fusion calling Checking" self.bpath=bpath self.npath=npath self.name='Novel' self.testcaseid=[] self.brespath=PathJF.getfullname_parent(os.path.join(self.bpath,'samples'),'result.txt','tophat_fusion') self.bfuspath=PathJF.getfullname_parent(os.path.join(self.bpath,'samples'),'fusion.out','tophat_main') self.nrespath=PathJF.getfullname_parent(os.path.join(self.npath,'samples'),'result.txt','tophat_fusion') self.nfuspath=PathJF.getfullname_parent(os.path.join(self.npath,'samples'),'fusion.out','tophat_main')
def __init__(self, bpath,npath): print "********************\n",strftime("%Y-%m-%d %H:%M:%S", gmtime()),"Start Differentail Expression Checking" self.bpath=bpath self.npath=npath self.name='DiffExp' self.testcaseid=[] self.bgenjsonpath=PathJF.getfullname_parent(os.path.join(self.bpath,'differential'),'Genes.json','cuffdiff') # find all the Genes.json file under the diffential folder self.btranjsonpath=PathJF.getfullname_parent(os.path.join(self.bpath,'differential'),'Transcripts.json','cuffdiff') # find all the Transcripts.json file under the diffential folder self.ngenjsonpath=PathJF.getfullname_parent(os.path.join(self.npath,'differential'),'Genes.json','cuffdiff') self.ntranjsonpath=PathJF.getfullname_parent(os.path.join(self.npath,'differential'),'Transcripts.json','cuffdiff')
def __init__(self, bpath,npath): print "********************\n",strftime("%Y-%m-%d %H:%M:%S", gmtime()),"Start Alignment Checking" self.bpath=bpath self.npath=npath self.name='Alignment' self.testcaseid=[] self.bsamalignpath=PathJF.getfullname_parent(os.path.join(self.bpath,'samples'),'Metrics.csv','sampled_alignment') self.nsamalignpath=PathJF.getfullname_parent(os.path.join(self.npath,'samples'),'Metrics.csv','sampled_alignment') self.bfullaligpath=PathJF.getfullname_parent(os.path.join(self.bpath,'samples'),'Metrics.csv','full_alignment') self.nfullaligpath=PathJF.getfullname_parent(os.path.join(self.npath,'samples'),'Metrics.csv','full_alignment') self.bbampath=PathJF.getfullname(self.npath,'bam') # file all the bam files self.nbampath=PathJF.getfullname(self.bpath,'bam')
def __init__(self, bpath,npath): print "********************\n",strftime("%Y-%m-%d %H:%M:%S", gmtime()),"Start Novel Transcript Checking" self.bpath=bpath self.npath=npath self.testcaseid=[] self.name='Novel assemblies' self.bisopath=PathJF.getfullname_parent(os.path.join(self.bpath,'samples'),'isoforms.fpkm_tracking','novel') self.bgenepath=PathJF.getfullname_parent(os.path.join(self.bpath,'samples'),'genes.fpkm_tracking','novel') self.bgtfpath=PathJF.getfullname_parent(os.path.join(self.bpath,'samples'),'merged.gtf','cuffmerge') self.nisopath=PathJF.getfullname_parent(os.path.join(self.npath,'samples'),'isoforms.fpkm_tracking','novel') self.ngenepath=PathJF.getfullname_parent(os.path.join(self.npath,'samples'),'genes.fpkm_tracking','novel') self.ngtfpath=PathJF.getfullname_parent(os.path.join(self.npath,'samples'),'merged.gtf','cuffmerge')