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Commit 5cf9276c authored by cmaffeo2's avatar cmaffeo2
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Sorta got something to work

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cadnano_segments.py
+ 20
− 165
View file @ 5cf9276c
......@@ -344,167 +344,6 @@ class cadnano_part(SegmentModel):
endList.append(lastStrand[1])
return endLists
def combineRegionLists(self,loHi1,loHi2,intersect=False):
"""Combines two lists of (lo,hi) pairs specifying integer
regions a single list of regions. """
## Validate input
for l in (loHi1,loHi2):
## Assert each region in lists is sorted
for pair in l:
assert(len(pair) == 2)
assert(pair[0] <= pair[1])
if len(loHi1) == 0:
if intersect:
return []
else:
return loHi2
if len(loHi2) == 0:
if intersect:
return []
else:
return loHi1
## Break input into lists of compact regions
compactRegions1,compactRegions2 = [[],[]]
for compactRegions,loHi in zip(
[compactRegions1,compactRegions2],
[loHi1,loHi2]):
tmp = []
lastHi = loHi[0][0]-1
for lo,hi in loHi:
if lo-1 != lastHi:
compactRegions.append(tmp)
tmp = []
tmp.append((lo,hi))
lastHi = hi
if len(tmp) > 0:
compactRegions.append(tmp)
## Build result
result = []
region = []
i,j = [0,0]
compactRegions1.append([[1e10]])
compactRegions2.append([[1e10]])
while i < len(compactRegions1)-1 or j < len(compactRegions2)-1:
cr1 = compactRegions1[i]
cr2 = compactRegions2[j]
## initialize region
if len(region) == 0:
if cr1[0][0] <= cr2[0][0]:
region = cr1
i += 1
continue
else:
region = cr2
j += 1
continue
if region[-1][-1] >= cr1[0][0]:
region = self.combineCompactRegionLists(region, cr1, intersect=False)
i+=1
elif region[-1][-1] >= cr2[0][0]:
region = self.combineCompactRegionLists(region, cr2, intersect=False)
j+=1
else:
result.extend(region)
region = []
assert( len(region) > 0 )
result.extend(region)
result = sorted(result)
# print("loHi1:",loHi1)
# print("loHi2:",loHi2)
# print(result,"\n")
if intersect:
lo = max( [loHi1[0][0], loHi2[0][0]] )
hi = min( [loHi1[-1][1], loHi2[-1][1]] )
result = [r for r in result if r[0] >= lo and r[1] <= hi]
return result
def combineCompactRegionLists(self,loHi1,loHi2,intersect=False):
"""Combines two lists of (lo,hi) pairs specifying regions within a
compact integer set into a single list of regions.
examples:
loHi1 = [[0,4],[5,7]]
loHi2 = [[2,4],[5,9]]
out = [(0, 1), (2, 4), (5, 7), (8, 9)]
loHi1 = [[0,3],[5,7]]
loHi2 = [[2,4],[5,9]]
out = [(0, 1), (2, 3), (4, 4), (5, 7), (8, 9)]
"""
## Validate input
for l in (loHi1,loHi2):
## Assert each region in lists is sorted
for pair in l:
assert(len(pair) == 2)
assert(pair[0] <= pair[1])
## Assert lists are compact
for pair1,pair2 in zip(l[::2],l[1::2]):
assert(pair1[1]+1 == pair2[0])
if len(loHi1) == 0:
if intersect:
return []
else:
return loHi2
if len(loHi2) == 0:
if intersect:
return []
else:
return loHi1
## Find the ends of the region
lo = min( [loHi1[0][0], loHi2[0][0]] )
hi = max( [loHi1[-1][1], loHi2[-1][1]] )
## Make a list of indices where each region will be split
splitAfter = []
for l,h in loHi2:
if l != lo:
splitAfter.append(l-1)
if h != hi:
splitAfter.append(h)
for l,h in loHi1:
if l != lo:
splitAfter.append(l-1)
if h != hi:
splitAfter.append(h)
splitAfter = sorted(list(set(splitAfter)))
# print("splitAfter:",splitAfter)
split=[]
last = -2
for s in splitAfter:
split.append(s)
last = s
# print("split:",split)
returnList = [(i+1,j) if i != j else (i,j) for i,j in zip([lo-1]+split,split+[hi])]
if intersect:
lo = max( [loHi1[0][0], loHi2[0][0]] )
hi = min( [loHi1[-1][1], loHi2[-1][1]] )
returnList = [r for r in returnList if r[0] >= lo and r[1] <= hi]
# print("loHi1:",loHi1)
# print("loHi2:",loHi2)
# print(returnList,"\n")
return returnList
def _helix_strands_to_segment_ranges(self, helix_strands):
"""Utility method to convert cadnano strand lists into list of
indices of terminal points"""
......@@ -595,24 +434,40 @@ class cadnano_part(SegmentModel):
## TODO: handle nicks that are at intrahelical connections(?)
zmid1 = int(0.5*(r1[0]+r1[1]))
zmid2 = int(0.5*(r2[0]+r2[1]))
if seg1.name == "19-3" or seg2.name == "19-3":
import pdb
pdb.set_trace()
# if zMid in strandOccupancies[0] and zMid in strandOccupancies[1]:
# seg = DoubleStrandedSegment(**kwargs,**posargs1)
# elif zMid in strandOccupancies[0]:
# seg = SingleStrandedSegment(**kwargs,**posargs1)
# elif zMid in strandOccupancies[1]:
# seg = SingleStrandedSegment(**kwargs,**posargs2)
## TODO: validate
if zmid1 in occ[0] and zmid2 in occ[0]:
seg1.connect_end3(seg2.start5)
if zmid1 in occ[1] and zmid2 in occ[1]:
if zmid1 in occ[0]:
seg2.connect_end3(seg1.end5)
end = seg1.end5
else:
end = seg1.start5
if zmid2 in occ[0]:
seg2.connect_start3(end)
else:
seg2.connect_end3(seg1.start5)
def _add_crossovers(self):
for h1,f1,z1,h2,f2,z2 in self.xover_list:
if (h1 == 52 or h2 == 52) and z1 == 221:
import pdb
pdb.set_trace()
# if (h1 == 52 or h2 == 52) and z1 == 221:
# import pdb
# pdb.set_trace()
seg1, nt1 = self._get_segment_nucleotide(h1,z1)
seg2, nt2 = self._get_segment_nucleotide(h2,z2)
## TODO: use different types of crossovers
## fwd?
seg1.add_crossover(nt1,seg2,nt2,[f1,f2])
def _add_prime_ends(self):
......
segmentmodel.py
+ 264
− 230
View file @ 5cf9276c
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