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')
