#!/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.")