def compare(self):
errornum=0
errormsg=''
[filenum,msg]=PathJF.check_pathlist(self.brespath,self.nrespath,'Novel','result.txt')
if msg !='':
return [0, msg,self.testcaseid]
else:
print str(filenum)+" result.txt file needs to be checked"
for i in range(len(self.brespath)):
[errornum1, errormsg1]=FileOverlap.CompFiles(Configurations_param.fusion_overlap_result_toler,self.brespath[i],self.nrespath[i],[0,1,2,3,4,5,6],' ') # result.txt checking
self.testcaseid.append(76745)
errornum=errornum+errornum1
errormsg=errormsg+'\n'+errormsg1
[filenum,msg]=PathJF.check_pathlist(self.bfuspath,self.nfuspath,'Novel','fusion.out')
if filenum==0: # if there is no file in baseline
print msg
return [0, '',self.testcaseid]
elif filenum !=0 and msg !='': # if there is file in baseline but not equal number of file in baseline and run foler
return [1,msg,self.testcaseid]
else:
for i in range(len(self.bfuspath)):
print "checking the fusion.out file under tophat_main: "+ self.bfuspath[i]+self.nfuspath[i]
[errornum2, errormsg2]=FileOverlap.CompFiles(Configurations_param.fusion_overlap_fusionout_toler,self.bfuspath[i],self.nfuspath[i],[0,1,2,3,4,5,6],' ') # fusion.out checking
self.testcaseid.append(76746)
errornum=errornum+errornum2
errormsg=errormsg+'\n'+errormsg2
if errornum>0:
return [1,'Fusion calling error: '+errormsg1+'\n'+errormsg2,self.testcaseid]
else:
return [0, '',list(set(self.testcaseid))]
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 compare(self):
[errornum,errormsg]=PathJF.folderchecking(self.bpath,self.npath) #Test if both two folders exist and the total number of folder is the same
self.testcaseid.append(76303)
if errornum >0:
return [errornum,errormsg,76303]
[errornum,errormsg]=PathJF.filechecking(self.bpath,self.npath) #1. Test if the total number of files is the same. 2. Test if the difference of the filesize beyone tolerance
self.testcaseid.append(76620)
self.testcaseid.append(76313)
if errornum >0:
return [errornum,errormsg,[76620,76313]]
[errornum,errormsg]=PathJF.csvchecking(self.bpath,self.npath) #Test if the content in the index.html is the identical or in tolerance range.
self.testcaseid.append(76691)
if errornum >0:
return [errornum,errormsg,76691]
#[errornum,errormsg]=PathJF.imagechecking(self.bpath,self.npath) #Test if the difference of two set of images are in tolerance range.
#self.testcaseid.append(77984)
if errornum >0:
return [errornum,errormsg,77984]
return [0, '',list(set(self.testcaseid))]
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')
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 getio(argv):
baselinefolder =''
newfolder = ''
testresultfolder = ''
if argv == None or len(argv) == 0:
print 'main.py -b <baseline run folder> -n <new run folder> -o <test result folder>'
sys.exit(1)
try:
opts, args = getopt.getopt(argv,"hb:n:o:",["baselinefolder=","newfolder=","testresultfolder="])
except getopt.GetoptError:
print 'main.py -b <baseline run folder> -n <new run folder> -o <test result folder>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'main.py -b <baseline run folder> -n <new run folder) -o <test result folder>'
sys.exit(3)
if opt in ("-b", "--baselinefolder"):
baselinefolder = arg
if opt in ("-n", "--newfolder"):
newfolder = arg
if opt in ("-o", "--testresultfolder"):
testresultfolder = PathJF.namebytime(arg)
if not os.path.isdir(testresultfolder):
try:
os.makedirs(testresultfolder)
except OSError:
print "can't make the test result folder"
sys.exit(4)
if os.path.exists(baselinefolder) and os.path.exists(newfolder):
print 'baseline run folder is ', baselinefolder
print 'new run folder is ', newfolder
print 'test result folder is ', testresultfolder
return [baselinefolder,newfolder,testresultfolder]
else:
print 'can not find the input baseline folder or new run folder!'
print 'Usage: main.py -b <baseline run folder> -n <new run folder>'
sys.exit(5)
