Merge pull request #1 from DKFZ-ODCF/fix-yet-another-bug-with-bad-data

Fix yet another bug with bad data

Author: vinjana

SophiaWorkflow.jar

@@ -1,2 +1,2 @@
 2.2
-0
+1

buildversion.txt

@@ -16,24 +16,25 @@
 # along with this program; if not, write to the Free Software
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
-from sys import argv,stderr
+from sys import argv, stderr
 from itertools import product
-preFilteredBedpe=argv[1]
 
-broadProd=list(product(range(51),range(51)))
-narrowProd=list(product(range(10),range(10)))
+preFilteredBedpe = argv[1]
 
-lineIndex=0
+broadProd = list(product(range(51), range(51)))
+narrowProd = list(product(range(10), range(10)))
+
+lineIndex = 0
 with open(preFilteredBedpe) as inputHandle:
     for line in inputHandle:
-        if line[0]!='#':
-            lineChunks=line.rstrip().split('\t')
-            eventType=lineChunks[8]
-            if lineChunks[0]==lineChunks[3] and eventType in {"TRA","DEL"}:
-                minPos=min(int(lineChunks[1]),int(lineChunks[4]))
-                maxPos=max(int(lineChunks[1]),int(lineChunks[4]))
-                eventScore=int(lineChunks[9])
+        if line[0] != '#':
+            lineChunks = line.rstrip().split('\t')
+            eventType = lineChunks[8]
+            if lineChunks[0] == lineChunks[3] and eventType in {"TRA", "DEL"}:
+                minPos = min(int(lineChunks[1]), int(lineChunks[4]))
+                maxPos = max(int(lineChunks[1]), int(lineChunks[4]))
+                eventScore = int(lineChunks[9])
                 for iterPair in broadProd:
-                    if (minPos-iterPair[0]) < maxPos-1+iterPair[1]:
-                        print(lineChunks[0],minPos-iterPair[0],maxPos-1+iterPair[1],lineIndex,sep='\t')
-            lineIndex+=1
+                    if (minPos - iterPair[0]) < maxPos - 1 + iterPair[1]:
+                        print(lineChunks[0], minPos - iterPair[0], maxPos - 1 + iterPair[1], lineIndex, sep='\t')
+            lineIndex += 1

resources/analysisTools/sophiaworkflow/RNAdecontaminationStep1.py

@@ -17,56 +17,59 @@
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
 
-from sys import argv,stderr
+from sys import argv, stderr
 from itertools import product
-preFilteredBedpe=argv[1]
-lineIndicesFile=argv[2]
+
+preFilteredBedpe = argv[1]
+lineIndicesFile = argv[2]
+
 
 def getIntronExonIndex(geneRawName):
-    geneChunks=geneRawName.split('_')
-    geneName="."
-    if geneChunks[0]!=".":
-        geneName='_'.join(geneChunks[:-1])
-    index=1
-    intronStatus="intron" in geneChunks[-1] or geneName=="."
-    if geneChunks[-1]!=".":
+    geneChunks = geneRawName.split('_')
+    geneName = "."
+    if geneChunks[0] != ".":
+        geneName = '_'.join(geneChunks[:-1])
+    index = 1
+    intronStatus = "intron" in geneChunks[-1] or geneName == "."
+    if geneChunks[-1] != ".":
         if "intron" in geneChunks[-1]:
-            index=int(geneChunks[-1].split('intron')[-1])
+            index = int(geneChunks[-1].split('intron')[-1])
         elif "exon" in geneChunks[-1]:
-            index=int(geneChunks[-1].split('exon')[-1])
-    return [geneName,index,intronStatus]
+            index = int(geneChunks[-1].split('exon')[-1])
+    return [geneName, index, intronStatus]
+
 
-lineIndices=set()
+lineIndices = set()
 with open(lineIndicesFile) as f:
     for line in f:
-        lineIndex=int(line.rstrip())
+        lineIndex = int(line.rstrip())
         lineIndices.add(lineIndex)
 
-lineIndex=-1
+lineIndex = -1
 with open(preFilteredBedpe) as inputHandle:
     for line in inputHandle:
-        if line[0]!='#':
-            lineIndex+=1
-            skipLine=False
+        if line[0] != '#':
+            lineIndex += 1
+            skipLine = False
             if lineIndex not in lineIndices:
-                lineChunks=line.rstrip().split('\t')
-                eventType=lineChunks[8]
-                eventScore=int(lineChunks[9])
-                if lineChunks[0]==lineChunks[3] and lineChunks[11]!="INV":
-                    gene1Raw=lineChunks[20]
-                    gene2Raw=lineChunks[30]
-                    gene1ListPre=[getIntronExonIndex(x) for x in [y.split(';')[0] for y in gene1Raw.split(',')] if '_' in x]
-                    gene2ListPre=[getIntronExonIndex(x) for x in [y.split(';')[0] for y in gene2Raw.split(',')] if '_' in x]
-                    for eventPair in product(gene1ListPre,gene2ListPre):
-                        if eventPair[0][0]==eventPair[1][0]:
-                            if eventPair[0][0]!=".":
+                lineChunks = line.rstrip().split('\t')
+                eventType = lineChunks[8]
+                eventScore = int(lineChunks[9])
+                if lineChunks[0] == lineChunks[3] and lineChunks[11] != "INV":
+                    gene1Raw = lineChunks[20]
+                    gene2Raw = lineChunks[30]
+                    gene1ListPre = [getIntronExonIndex(x) for x in [y.split(';')[0] for y in gene1Raw.split(',')] if '_' in x]
+                    gene2ListPre = [getIntronExonIndex(x) for x in [y.split(';')[0] for y in gene2Raw.split(',')] if '_' in x]
+                    for eventPair in product(gene1ListPre, gene2ListPre):
+                        if eventPair[0][0] == eventPair[1][0]:
+                            if eventPair[0][0] != ".":
                                 if (eventPair[0][2] or eventPair[1][2]):
-                                    if abs(eventPair[0][1]-eventPair[1][1])<2:
-                                        skipLine=True
+                                    if abs(eventPair[0][1] - eventPair[1][1]) < 2:
+                                        skipLine = True
                                         break
                                 else:
-                                    if eventType=="DEL" and abs(eventPair[0][1]-eventPair[1][1])==1:
-                                        skipLine=True
+                                    if eventType == "DEL" and abs(eventPair[0][1] - eventPair[1][1]) == 1:
+                                        skipLine = True
                                         break
                 if not skipLine:
                     print(line.rstrip())