From 0603388211cf14bcf1a6166204cbfd0748d991ab Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Thu, 27 Sep 2018 14:10:55 -0500
Subject: [PATCH] Fixed two issues with ssDNA cadnano reader.
First, ssDNA segments are now broken at crossovers
Second, ssDNA segments aren't allowed to stack intrahelically
---
mrdna/readers/cadnano_segments.py | 74 +++++++++++++++++++++++++------
1 file changed, 61 insertions(+), 13 deletions(-)
diff --git a/mrdna/readers/cadnano_segments.py b/mrdna/readers/cadnano_segments.py
index 7a163a0..bc4a50f 100644
--- a/mrdna/readers/cadnano_segments.py
+++ b/mrdna/readers/cadnano_segments.py
@@ -226,7 +226,10 @@ class cadnano_part(SegmentModel):
vh_list = []
strand_list = []
- self.xover_list = xover_list = []
+ xover_list = []
+ self.xovers_from = dict()
+ self.xovers_to = dict()
+
try:
numHID = part.getMaxIdNum() + 1
except:
@@ -247,9 +250,16 @@ class cadnano_part(SegmentModel):
fwd_ss, rev_ss = part.getStrandSets(id_num)
fwd_idxs, fwd_colors = fwd_ss.dump(xover_list)
rev_idxs, rev_colors = rev_ss.dump(xover_list)
-
strand_list.append((fwd_idxs, rev_idxs))
+ self.xovers_from[id_num] = []
+ self.xovers_to[id_num] = []
+
+ for xo in xover_list:
+ h1,f1,z1,h2,f2,z2 = xo
+ self.xovers_from[h1].append(xo)
+ self.xovers_to[h2].append(xo)
+
## Get lists of 5/3prime ends
strands5 = [o.strand5p() for o in part.oligos()]
strands3 = [o.strand3p() for o in part.oligos()]
@@ -274,7 +284,8 @@ class cadnano_part(SegmentModel):
## Build list of tuples containing (idx,length) of insertions/skips
insertions = sorted( [(i[0],i[1].length()) for i in allInsertions[hid].items()],
key=lambda x: x[0] )
-
+
+ ## TODO: make the following code (until "regions = ...") more readable
## Build list of strand ends and list of mandatory node locations
ends1,ends2 = self._helixStrandsToEnds(helixStrands)
@@ -290,9 +301,28 @@ class cadnano_part(SegmentModel):
ends1,ends2 = [ [(e[i],e[i+1]) for i in range(0,len(e),2)] for e in (ends1,ends2) ]
regions = combineRegionLists(ends1,ends2)
+
+ ## Split regions in event of ssDNA crossover
+ split_regions = []
+ for zid1,zid2 in regions:
+ zMid = int(0.5*(zid1+zid2))
+ if zMid in strandOccupancies[0] and zMid in strandOccupancies[1]:
+ split_regions.append( (zid1,zid2) )
+ else:
+ is_fwd = zMid in strandOccupancies[0]
+ ends = [z for h,f,z in self._get_crossover_locations( hid, range(zid1+1,zid2), is_fwd )]
+ z1 = zid1
+ for z in sorted(ends):
+ z2 = z
+ if z2 > z1:
+ split_regions.append( (z1,z2) )
+ z1 = z2+1
+ z2 = zid2
+ if z2 > z1: split_regions.append( (z1,z2) )
+
# if hid == 43:
# import pdb
- for zid1,zid2 in regions:
+ for zid1,zid2 in split_regions:
zMid = int(0.5*(zid1+zid2))
assert( zMid in strandOccupancies[0] or zMid in strandOccupancies[1] )
@@ -482,6 +512,8 @@ class cadnano_part(SegmentModel):
occ = self.strand_occupancies[hid]
for i in range(len(segs)-1):
seg1,seg2 = [segs[j] for j in (i,i+1)]
+ if isinstance(seg1,SingleStrandedSegment) and isinstance(seg2,SingleStrandedSegment):
+ continue
r1,r2 = [self.helix_ranges[hid][j] for j in (i,i+1)]
if r1[1]+1 == r2[0]:
## TODO: handle nicks that are at intrahelical connections(?)
@@ -502,16 +534,32 @@ class cadnano_part(SegmentModel):
else:
seg2.connect_end3(end)
+
+ def _get_crossover_locations(self, helix_idx, nt_idx_range, fwd_strand=None):
+ xos = []
+ def append_if_in_range(h,f,z):
+ if fwd_strand in (None,f) and z in nt_idx_range:
+ xos.append((h,f,z))
+
+ for xo in self.xovers_from[helix_idx]:
+ ## h1,f1,z1,h2,f2,z2 = xo[3:]
+
+ append_if_in_range(*xo[:3])
+ for xo in self.xovers_to[helix_idx]:
+ append_if_in_range(*xo[3:])
+ return xos
+
def _add_crossovers(self):
- for h1,f1,z1,h2,f2,z2 in self.xover_list:
- seg1, nt1 = self._get_segment_nucleotide(h1,z1,not f1)
- seg2, nt2 = self._get_segment_nucleotide(h2,z2,f2)
- ## TODO: use different types of crossovers
- ## fwd?
- ## 5'-to-3' direction
- if isinstance(seg1, SingleStrandedSegment): f1 = True
- if isinstance(seg2, SingleStrandedSegment): f2 = True
- seg1.add_crossover(nt1,seg2,nt2,[f1,f2])
+ for hid,xos in self.xovers_from.items():
+ for h1,f1,z1,h2,f2,z2 in xos:
+ seg1, nt1 = self._get_segment_nucleotide(h1,z1,not f1)
+ seg2, nt2 = self._get_segment_nucleotide(h2,z2,f2)
+ ## TODO: use different types of crossovers
+ ## fwd?
+ ## 5'-to-3' direction
+ if isinstance(seg1, SingleStrandedSegment): f1 = True
+ if isinstance(seg2, SingleStrandedSegment): f2 = True
+ seg1.add_crossover(nt1,seg2,nt2,[f1,f2])
def _add_prime_ends(self):
for h,fwd,z in self._5prime_list:
--
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