def runPipeClip(infile,outputPrefix,matchLength,mismatch,rmdup,fdrEnrichedCluster,clipType,fdrReliableMutation,species):
myClip = CLIP.CLIP(infile,outputPrefix)
logging.info("Start to run")
if myClip.testInput():#check input
logging.info("Input file OK,start to run PIPE-CLIP")
logging.info("Species info %s" % species)
if myClip.readfile():
myClip.filter(matchLength,mismatch,clipType,rmdup,outputPrefix)
myClip.printMutations()
if len(myClip.clusters)>0:
logging.info("Get enriched clusters")
gc.collect()
status = Enrich.clusterEnrich(myClip,fdrEnrichedCluster)
if status:
logging.info("Found %d enriched clusters" % myClip.sigClusterCount)
myClip.printEnrichedClusters()
else:
logging.error("There is no enriched cluster found. Exit program")
sys.exit(1)
else:
logging.error("There is no clusters found. Please check input.Exit program.")
sys.exit(1)
if len(myClip.mutations.keys())>0:
logging.info("Get reliable mutations")
Enrich.mutationEnrich(myClip,fdrReliableMutation)
myClip.printReliableMutations()
else:
logging.warning("There is no mutation found in this BAM file.")
#Start to get crosslinking sites
if myClip.sigClusterCount > 0 and myClip.sigMutationCount>0:
logging.info("Get cross-linking sites")
myClip.getCrosslinking()
if (len(myClip.crosslinking.keys())>0):
outfilelist = myClip.printCrosslinkingSites()
myClip.printCrosslinkingMutations()
else:
logging.warning("There is no crosslinking found. May be caused by no reliable mutations in enriched clusters. Print out enriched clusters instead.")
outfilelist = myClip.printEnrichClusters()
else:
if myClip.sigClusterCount <= 0:
logging.error("There is no enriched clusters for this sample, please check your input file. Exit.")
sys.exit(2)
elif myClip.sigMutationCount <=0:
logging.warning("There is no reliable mutations found. PIPE-CLIP will provide enriched clusters as crosslinking candidates.")
outfilelist = myClip.printEnrichClusters()
#annotation if possible
#logging.debug(outfilelist)
if species in ["mm10","mm9","hg19"]:
for name in outfilelist:
#logging.debug("Start to do annotation for %s" % name)
Utils.annotation(name,species)
else:
print >> sys.stderr, "File corruputed, program exit."
sys.exit(0)
def fishertest(self): fp = Enrich.fisherTest(self.clusterP,self.mutationP) self.fisherP = fp
