#!/usr/bin/python import pipeclip pipeclip.runPipeClip('2_mapped.bam','2',10,2,0,0.01,1,0.01,None) print 'Done!'
#!/usr/bin/python import pipeclip pipeclip.runPipeClip('2_mapped.bam', '2', 10, 2, 0, 0.01, 1, 0.01, None) print 'Done!'
def processCommandArgs(): infile = bamFileEntryString.get() outputPrefix = prefixEntryString.get() matchLength = matchLenString.get() mismatch = maxMismatchString.get() fdrCluster = fdrEnrichedClusterString.get() fdrMutation = fdrReliableMutationString.get() error = False if not len(pcrRemovalListbox.curselection()) > 0: if not error: popupError("Please chhose a PCR Removal") error = True else: pcr = pcrRemovalListbox.curselection()[0] if not len(clipTypeListbox.curselection()) > 0: if not error: popupError("Please choose a clip type") error = True else: clipType = clipTypeListbox.curselection()[0] #if not len(speciesListbox.curselection()) > 0: # if not error: # popupError("PLease selection a species") # error = True #else: # species = speciesListbox.curselection()[0] if not re.match('[1-4]',mismatch,flags=0): if not error: popupError("Invalid mismatch parameter; Value Range: [1,4]") error = True if not re.match('\d+',matchLength,flags=0): if not error: popupError("Invalid match length parameter") error = True else: if(int(matchLength) < 10): popupError("Expected range of values for match length parameter: [10,)"); error = True if not re.match('0?\.\d+',fdrCluster,flags=0): if not error: popupError("Invalid fdr cluster; Expected Value: (0,1)") error = True if not re.match('0?\.\d+',fdrMutation,flags=0): if not error: popupError("Invalid fdr mutation parameter; Expected Value: (0,1)") error = True if not re.search('\.bam$',infile,flags=0): if not error: popupError("Invalid BAM File") error = True if not re.match('^[a-zA-Z0-9\/]+$',outputPrefix,flags=0): if not error: popupError("Invalid output prefix, must follow regex: ^[a-zA-Z0-9\/]+$") error = True if not error: import pipeclip pipeclip.runPipeClip(infile,outputPrefix,int(matchLength),int(mismatch),int(pcr),float(fdrCluster),int(clipType),float(fdrMutation),None) popup("Success","Done with analysis.")