From 6a314a50bd991bb8ec3353fc0992ea5bfe1faf92 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Sun, 23 Sep 2018 16:00:41 -0500
Subject: [PATCH] Fixed some small issues with cadnano reader for ssDNA
---
mrdna/readers/cadnano_segments.py | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/mrdna/readers/cadnano_segments.py b/mrdna/readers/cadnano_segments.py
index 0d366b8..15dd725 100644
--- a/mrdna/readers/cadnano_segments.py
+++ b/mrdna/readers/cadnano_segments.py
@@ -226,7 +226,10 @@ class cadnano_part(SegmentModel):
numHID = part.getIdNumMax() + 1
for id_num in range(numHID):
- offset_and_size = part.getOffsetAndSize(id_num)
+ try:
+ offset_and_size = part.getOffsetAndSize(id_num)
+ except:
+ offset_and_size = None
if offset_and_size is None:
## Add a placeholder for empty helix
vh_list.append((id_num, 0))
@@ -499,16 +502,20 @@ class cadnano_part(SegmentModel):
## 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:
seg, nt = self._get_segment_nucleotide(h,z, fwd)
+ if isinstance(seg, SingleStrandedSegment): fwd = True
# print("adding 5prime",seg.name,nt,fwd)
seg.add_5prime(nt,fwd)
for h,fwd,z in self._3prime_list:
seg, nt = self._get_segment_nucleotide(h,z, not fwd)
+ if isinstance(seg, SingleStrandedSegment): fwd = True
# print("adding 3prime",seg.name,nt,fwd)
seg.add_3prime(nt,fwd)
--
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