From 556b37e1eebcb3400ad7b61e3be3a4b84ee50b06 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 18 Sep 2018 16:39:44 -0500
Subject: [PATCH] Improved strand routing algorithm when a 5prime or 3prime
location has a connection
---
mrdna/segmentmodel.py | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 650e5a5..24633ae 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -696,7 +696,7 @@ class Segment(ConnectableElement, Group):
if l.is_3prime_side_of_connection: continue
## Stop if we found the 3prime end
- if l.on_fwd_strand == is_fwd and l.type_ == "3prime":
+ if l.on_fwd_strand == is_fwd and l.type_ == "3prime" and l.connection is None:
# print(" found end at",l)
return pos, None, None, None, None
@@ -2429,18 +2429,23 @@ class SegmentModel(ArbdModel):
break
except:
print("Unexpected error:", sys.exc_info()[0])
+ # import pdb
+ # pdb.set_trace()
+ # seg.get_strand_segment(pos, is_fwd, move_at_least)
+ # strand.add_dna(seg, pos, end_pos, is_fwd)
raise
if next_seg is None:
break
else:
seg,pos,is_fwd = (next_seg, next_pos, next_dir)
+ strand.history = list(history)
return history
strand_counter = 0
history = []
for seg in self.segments:
- locs = seg.get_5prime_locations()
+ locs = filter(lambda l: l.connection is None, seg.get_5prime_locations())
if locs is None: continue
# for pos, is_fwd in locs:
for l in locs:
--
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