From 39425b0c3a6108a4b9eb902792fac24154a7c6d7 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 17 Aug 2018 16:02:59 -0500
Subject: [PATCH] fixup: Enabled automatic creation of terminal...
---
segmentmodel.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/segmentmodel.py b/segmentmodel.py
index ad712c1..16906cd 100644
--- a/segmentmodel.py
+++ b/segmentmodel.py
@@ -2059,17 +2059,17 @@ class SegmentModel(ArbdModel):
""" Ensure unconnected ends have 5prime Location objects """
for seg in self.segments:
## TODO move into Segment calls
- five_prime_locs = seg.get_locations("5prime")
- three_prime_locs = seg.get_locations("3prime")
+ five_prime_locs = sum([seg.get_locations(s) for s in ("5prime","crossover","terminal_crossover")],[])
+ three_prime_locs = sum([seg.get_locations(s) for s in ("3prime","crossover","terminal_crossover")],[])
def is_start_5prime(l):
return l.get_nt_pos() < 1 and l.on_fwd_strand
def is_end_5prime(l):
- return l.get_nt_pos() > seg.num_nt-1 and not l.on_fwd_strand
+ return l.get_nt_pos() > seg.num_nt-2 and not l.on_fwd_strand
def is_start_3prime(l):
return l.get_nt_pos() < 1 and not l.on_fwd_strand
def is_end_3prime(l):
- return l.get_nt_pos() > seg.num_nt-1 and l.on_fwd_strand
+ return l.get_nt_pos() > seg.num_nt-2 and l.on_fwd_strand
if seg.start5.connection is None:
if len(list(filter( is_start_5prime, five_prime_locs ))) == 0:
--
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