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Checks if one interval contains any overlap with another interval. Keyword arguments: t1 -- First tuple. t2 -- Second tuple. Returns: Returns -1 if i1 is before i2; 1 if i1 is after i2; and 0 if there is any overlap.

def overlap(t1, t2): """Checks if one interval contains any overlap with another interval. Keyword arguments: t1 -- First tuple. t2 -- Second tuple. Returns: Returns -1 if i1 is before i2; 1 if i1 is after i2; and 0 if there is any overlap. """ if(t1[1] <= t2[0]): return -1 # interval1 is before interval2 if(t2[1] <= t1[0]): return 1 # interval1 is after interval2 return 0 # interval1 overlaps interval2

**cadnano2**(Download)

l0, h0 = strand0.idxs() l1, h1 = strand1.idxs() oLow, oHigh = util.overlap(l0, h0, l1, h1) try: lList = filter(lambda x:x>oLow and x<oHigh, part.getPreXoversLow(strandType, p0))

src/c/a/cadnano2-HEAD/model/strand.py

**cadnano2**(Download)

# get the ovelap lowIdx, highIdx = util.overlap(sLowIdx, sHighIdx, cLowIdx, cHighIdx) # only get the characters we're using, while we're at it, make it the

src/m/o/MotifAnalysisPackage-0.0.1/motifStatistics/genome.py

**MotifAnalysisPackage**(Download)

didBreak = False while(counter < len(assocDict[chrName])): check = util.overlap(coord,assocDict[chrName][counter]) if(check == 0): # Contain overlap didBreak = True

else: geneCoord = [assocDict[chrName][counter][0],assocDict[chrName][counter][1]+promoterLength] check = util.overlap(coord,geneCoord) # Check overlap between coordinate and gene+promoter if(check == 0): # If contain overlap, then check if the coordinate also contains overlap with the next gene

if(assocDict[chrName][counter+1][4] == "+"): geneCoordNext = [assocDict[chrName][counter+1][0]-promoterLength,assocDict[chrName][counter+1][1]] else: geneCoordNext = [assocDict[chrName][counter+1][0],assocDict[chrName][counter+1][1]+promoterLength] checkNext = util.overlap(coord,geneCoordNext) # Verify overlap between coordinate and next gene if(checkNext == 0): genesList.append(assocDict[chrName][counter+1][2]+"_PROX") # If there is an overlap then add this gene to association list #else: # If this is the last gene (there is no 'next') then dont verify overlap

genesList = [] # List of overlapping genes maxGeneCoord = [geneCoord[0]-threshDist,geneCoord[1]+threshDist] maxCheck = util.overlap(coord,maxGeneCoord) if(maxCheck == 0): genesList.append(assocDict[chrName][counter][2]+"_DIST") # If it overlapped then put current gene in overlap list

else: geneCoordPrev = [assocDict[chrName][counter-1][0],assocDict[chrName][counter-1][1]+promoterLength] maxGeneCoordPrev = [geneCoordPrev[0]-threshDist,geneCoordPrev[1]+threshDist] maxCheckPrev = util.overlap(coord,maxGeneCoordPrev) if(maxCheckPrev == 0): genesList.append(assocDict[chrName][counter-1][2]+"_DIST") # If it overlapped then put previous gene in overlap list

src/m/o/MotifAnalysisPackage-0.0.1/motifStatistics/motif.py

**MotifAnalysisPackage**(Download)

while(counter[factorName] < len(allMpbsDict[factorName][chrName])): currMpbs = allMpbsDict[factorName][chrName][counter[factorName]] check = util.overlap(coord,currMpbs) if(check == 0): # Contain overlap flagMotifs[factorName] = True