def nxPerformBreaks(oligo, breakItems, tokenList, startingToken,
minStapleLegLen):
""" fullBreakptSoln is in the format of an IBS (see breakStrands).
This function performs the breaks proposed by the solution. """
part = oligo.part()
if breakItems:
util.beginSuperMacro(part, desc="Auto-Break")
# temp = []
# for s in oligo.strand5p().generator3pStrand():
# temp.append(s.length())
# print "the segments", sum(temp), temp
# print "the sum is ", sum(breakList[1]), "==", oligo.length(), "isLoop", oligo.isLoop()
# print "the breakItems", breakItems
strand = oligo.strand5p()
if oligo.isLoop():
# start things off make first cut
length0 = sum(tokenList[0:startingToken + 1])
strand, idx, is5to3 = getStrandAtLengthInOligo(
strand, length0 - minStapleLegLen)
sS = strand.strandSet()
found, sSIdx = sS.getStrandIndex(strand)
# found, overlap, sSIdx = sS._findIndexOfRangeFor(strand)
strand.split(idx, updateSequence=False)
strand = sS._strandList[sSIdx +
1] if is5to3 else sS._strandList[sSIdx]
# now iterate through all the breaks
for b in breakItems[0:-1]:
if strand.oligo().length() > b:
strand, idx, is5to3 = getStrandAtLengthInOligo(strand, b)
sS = strand.strandSet()
found, sSIdx = sS.getStrandIndex(strand)
# found, overlap, sSIdx = sS._findIndexOfRangeFor(strand)
strand.split(idx, updateSequence=False)
strand = sS._strandList[sSIdx +
1] if is5to3 else sS._strandList[sSIdx]
else:
raise Exception(
"Oligo length %d is shorter than break length %d" %
(strand.oligo().length(), b))
util.endSuperMacro(part)
def performBreaks(part, fullBreakptSoln):
""" fullBreakptSoln is in the format of an IBS (see breakStrands).
This function performs the breaks proposed by the solution. """
util.beginSuperMacro(part, desc="Auto-Break")
breakList, oligo = [], None # Only for logging purposes
if fullBreakptSoln != None: # Skip the first breakpoint
fullBreakptSoln = fullBreakptSoln[1]
while fullBreakptSoln != None:
curNode = fullBreakptSoln[2]
fullBreakptSoln = fullBreakptSoln[1] # Walk up the linked list
if fullBreakptSoln == None: # Skip last breakpoint
break
pos, strand, idx, isTerminal = curNode
if strand.isDrawn5to3():
idx -= 1 # Our indices correspond to the left side of the base
strand.split(idx, updateSequence=False)
breakList.append(curNode) # Logging purposes only
# print 'Breaks for %s at: %s'%(oligo, ' '.join(str(p) for p in breakList))
util.endSuperMacro(part)
def performBreaks(part, fullBreakptSoln):
""" fullBreakptSoln is in the format of an IBS (see breakStrands).
This function performs the breaks proposed by the solution. """
util.beginSuperMacro(part, desc="Auto-Break")
breakList, oligo = [], None # Only for logging purposes
if fullBreakptSoln != None: # Skip the first breakpoint
fullBreakptSoln = fullBreakptSoln[1]
while fullBreakptSoln != None:
curNode = fullBreakptSoln[2]
fullBreakptSoln = fullBreakptSoln[1] # Walk up the linked list
if fullBreakptSoln == None: # Skip last breakpoint
break
pos, strand, idx, isTerminal = curNode
if strand.isDrawn5to3():
idx -= 1 # Our indices correspond to the left side of the base
strand.split(idx, updateSequence=False)
breakList.append(curNode) # Logging purposes only
# print 'Breaks for %s at: %s'%(oligo, ' '.join(str(p) for p in breakList))
util.endSuperMacro(part)
def mouseReleaseEvent(self, event):
"""docstring for mouseReleaseEvent"""
part = self.part()
uS = part.undoStack()
strands = []
# Look at the undo stack in reverse order
for i in range(uS.index()-1, 0, -1):
# Check for contiguous strand additions
m = _strand_re.match(uS.text(i))
if m:
strands.insert(0, map(int, m.groups()))
else:
break
if len(strands) > 1:
autoScafType = app().prefs.getAutoScafType()
util.beginSuperMacro(part, "Auto-connect")
if autoScafType == "Mid-seam":
self.autoScafMidSeam(strands)
elif autoScafType == "Raster":
self.autoScafRaster(strands)
util.endSuperMacro(part)
def nxPerformBreaks(oligo, breakItems, tokenList, startingToken, minStapleLegLen):
""" fullBreakptSoln is in the format of an IBS (see breakStrands).
This function performs the breaks proposed by the solution. """
part = oligo.part()
if breakItems:
util.beginSuperMacro(part, desc="Auto-Break")
# temp = []
# for s in oligo.strand5p().generator3pStrand():
# temp.append(s.length())
# print "the segments", sum(temp), temp
# print "the sum is ", sum(breakList[1]), "==", oligo.length(), "isLoop", oligo.isLoop()
# print "the breakItems", breakItems
strand = oligo.strand5p()
if oligo.isLoop():
# start things off make first cut
length0 = sum(tokenList[0:startingToken+1])
strand, idx, is5to3 = getStrandAtLengthInOligo(strand, length0-minStapleLegLen)
sS = strand.strandSet()
found, sSIdx = sS.getStrandIndex(strand)
# found, overlap, sSIdx = sS._findIndexOfRangeFor(strand)
strand.split(idx, updateSequence=False)
strand = sS._strandList[sSIdx+1] if is5to3 else sS._strandList[sSIdx]
# now iterate through all the breaks
for b in breakItems[0:-1]:
if strand.oligo().length() > b:
strand, idx, is5to3 = getStrandAtLengthInOligo(strand, b)
sS = strand.strandSet()
found, sSIdx = sS.getStrandIndex(strand)
# found, overlap, sSIdx = sS._findIndexOfRangeFor(strand)
strand.split(idx, updateSequence=False)
strand = sS._strandList[sSIdx+1] if is5to3 else sS._strandList[sSIdx]
else:
raise Exception("Oligo length %d is shorter than break length %d" % (strand.oligo().length(), b))
util.endSuperMacro(part)