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bug fix with relation to classes

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sroos
sroos committed Apr 3, 2014
1 parent 95b275d commit 05e3fb6d7c20e8c6b980f5738eab6ab68d9d2e80
Showing with 31 additions and 82,629 deletions.
  1. +1 −0 .gitignore
  2. +3 −3 getCrosslinking.py
  3. +18 −18 gui.py
  4. +0 −49,498 hg19.RefSeq.bed
  5. +0 −37 inputprocess_test.py
  6. +0 −33,064 mm10.RefSeq.bed
  7. +9 −9 pipeclip.py
@@ -1,2 +1,3 @@
*.pyc
*.pdf
.DS_Store
@@ -40,7 +40,7 @@ def fisherTest(p):
return fps

def run(self):
bed_merge = cluster_bed.intersect(mutation_bed,wao=True)
bed_merge = self.cluster_bed.intersect(self.mutation_bed,wao=True)
overlap = {}
mutationLoc = {}
kms = {}
@@ -78,8 +78,8 @@ def getCrossLinkingMain(cluster_bed_path,mutation_bed_path,producedFilePath):
sys.exit(1)

producedFile = open(producedFilePath,"w+")
crossLinkingRunner = crossLinkingRunner(cluster_bed,mutation_bed,producedFile)
crossLinkingRunner.run()
acrossLinkingRunner = crossLinkingRunner(cluster_bed,mutation_bed,producedFile)
acrossLinkingRunner.run()

def crossLinkingRunnerMain():
try:
36 gui.py
@@ -23,9 +23,10 @@ def BAMFileSelectionCallback():
def PreBAMFileSelectionCallback():
thread = threading.Thread(target=BAMFileSelectionCallback)
thread.start()

def popup(title,msg):
tkMessageBox.showinfo(title,msg)
def popupError(msg):
tkMessageBox.showinfo("Parameter Error",msg)
popup("Parameter Error",msg)

row = 0
col = 0
@@ -68,13 +69,13 @@ def popupError(msg):
fdrReliableMutationEntry = Entry(root,bd=3,textvariable=fdrReliableMutationString).grid(row=row,column=1)
row += 1

speciesLabel = Label(root,bd=3,text="Species").grid(row=row,column=0)
speciesListbox = Listbox(root,selectmode="single",height=3,exportselection=0)
speciesListbox.insert(0,"mm10")
speciesListbox.insert(1,"hg19")
speciesListbox.insert(1,"mm9")
speciesListbox.grid(row=row,column=1)
row += 1
#speciesLabel = Label(root,bd=3,text="Species").grid(row=row,column=0)
#speciesListbox = Listbox(root,selectmode="single",height=3,exportselection=0)
#speciesListbox.insert(0,"mm10")
#speciesListbox.insert(1,"hg19")
#speciesListbox.insert(1,"mm9")
#speciesListbox.grid(row=row,column=1)
#row += 1

bamFileButton = Button(root,text="Select BAM File",command = PreBAMFileSelectionCallback).grid(row=row,column=0)
bamFileEntry = Entry(root, bd=3,textvariable=bamFileEntryString,state=DISABLED).grid(row=(row),column=1)
@@ -102,12 +103,12 @@ def processCommandArgs():
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 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:
@@ -144,10 +145,9 @@ def processCommandArgs():
error = True

if not error:
print "Running analysis"
import pipeclip
pipeclip.runPipeClip(infile,outputPrefix,int(matchLength),int(mismatch),int(pcr),float(fdrCluster),int(clipType),float(fdrMutation),species)
print "Done with analysis"
pipeclip.runPipeClip(infile,outputPrefix,int(matchLength),int(mismatch),int(pcr),float(fdrCluster),int(clipType),float(fdrMutation),None)
popup("Success","Done with analysis. Output can be found in"+outputPrefix)

def runGui(runButton):
runButton.configure(state=NORMAL,text="Run")
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