From 7bc1eb139a5c15a52cc6d500cd194cfb70b0e343 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 10 Jul 2018 17:53:08 -0500
Subject: [PATCH] Fixed issues with skips at crossovers, but needs testing
---
cadnano_segments.py | 35 +++++++++++++++++++++++++----------
segmentmodel.py | 7 +++----
2 files changed, 28 insertions(+), 14 deletions(-)
diff --git a/cadnano_segments.py b/cadnano_segments.py
index 35db031..e261920 100644
--- a/cadnano_segments.py
+++ b/cadnano_segments.py
@@ -247,7 +247,7 @@ class cadnano_part(SegmentModel):
rev_idxs, rev_colors = rev_ss.dump(xover_list)
strand_list.append((fwd_idxs, rev_idxs))
-
+
## Get lists of 5/3prime ends
strands5 = [o.strand5p() for o in part.oligos()]
strands3 = [o.strand3p() for o in part.oligos()]
@@ -401,7 +401,7 @@ class cadnano_part(SegmentModel):
nt += self.insertions[hid][i].length()
return nt
- def _get_segment_nucleotide(self, hid, zid):
+ def _get_segment_nucleotide(self, hid, zid, get_forward_location=False):
""" returns segments and zero-based nucleotide index """
seg = self._get_segment(hid,zid)
sid = self.helices[hid].index(seg)
@@ -409,23 +409,36 @@ class cadnano_part(SegmentModel):
zMid = int(0.5*(zmin+zmax))
occ = self.strand_occupancies[hid]
+ ins = self.insertions[hid]
## TODO combine if/else when nested TODO is resolved
+ # if zid in self.insertions[hid]:
+ # import pdb
+ # pdb.set_trace()
+
if (zMid not in occ[0]) and (zMid in occ[1]):
## reversed ssDNA strand
nt = zmax-zid
# TODO: for i in range(zmin,zid+1): ?
- for i in range(zid,zmax):
+ for i in range(zid,zmax+1):
if i in self.insertions[hid]:
nt += self.insertions[hid][i].length()
else:
## normal condition
+ if get_forward_location:
+ while zid in ins and ins[zid].length() < 0 and zid <= zmax:
+ zid+=1
+ # else:
+ # while zid in ins and ins[zid].length() > 0 and zid >= zmax:
+ # zid-=1
nt = zid-zmin
- # TODO: for i in range(zmin,zid+1): ?
for i in range(zmin,zid):
- if i in self.insertions[hid]:
- nt += self.insertions[hid][i].length()
+ if i in ins:
+ nt += ins[i].length()
+ if not get_forward_location and zid in ins:
+ nt += ins[zid].length()
+
## Find insertions
return seg, nt
@@ -464,12 +477,14 @@ class cadnano_part(SegmentModel):
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()
- seg1, nt1 = self._get_segment_nucleotide(h1,z1)
- seg2, nt2 = self._get_segment_nucleotide(h2,z2)
+ if (h1 == 15 and z1 == 230) or h2 == 15 and z2 == 231:
+ import pdb
+ pdb.set_trace()
+ 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
seg1.add_crossover(nt1,seg2,nt2,[f1,f2])
def _add_prime_ends(self):
diff --git a/segmentmodel.py b/segmentmodel.py
index d8bb260..232aad6 100644
--- a/segmentmodel.py
+++ b/segmentmodel.py
@@ -1047,10 +1047,9 @@ class Strand(Group):
## TODO disambiguate names of functions
def add_dna(self, segment, start, end, is_fwd):
- # TODOTODO use nt pos ?
- """ start/end should be provided expressed as contour_length, is_fwd tuples """
- if not (segment.contour_to_nt_pos(np.abs(start-end)) > 0.9):
- print( "WARNING: segment constructed with a very small number of nts ({})".format(segment.contour_to_nt_pos(np.abs(start-end))) )
+ """ start/end are given as nt """
+ if np.abs(start-end) <= 0.9:
+ print( "WARNING: segment constructed with a very small number of nts ({})".format(np.abs(start-end)) )
# import pdb
# pdb.set_trace()
for s in self.strand_segments:
--
GitLab