From e440cc78dafd6927275b5541836cd5744623553a Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 17 Aug 2018 15:02:23 -0500
Subject: [PATCH] Enabled automatic creation of terminal 5prime and 3prime ends
---
segmentmodel.py | 62 +++++++++++++++++++++----------------------------
1 file changed, 27 insertions(+), 35 deletions(-)
diff --git a/segmentmodel.py b/segmentmodel.py
index 4f17c64..9e34112 100644
--- a/segmentmodel.py
+++ b/segmentmodel.py
@@ -2061,41 +2061,33 @@ class SegmentModel(ArbdModel):
""" Ensure unconnected ends have 5prime Location objects """
for seg in self.segments:
## TODO move into Segment calls
- import pdb
- if False: # TODO: Make this happen conditionally
- if seg.start5.connection is None:
- add_end = True
- for l in seg.get_locations("5prime"):
- if l.address == 0 and l.on_fwd_strand:
- add_end = False
- break
- if add_end:
- seg.add_5prime(0)
- if 'end5' in seg.__dict__ and seg.end5.connection is None:
- add_end = True
- for l in seg.get_locations("5prime"):
- if l.address == 1 and (l.on_fwd_strand is False):
- add_end = False
- break
- if add_end:
- seg.add_5prime(seg.num_nt-1,on_fwd_strand=False)
-
- if 'start3' in seg.__dict__ and seg.start3.connection is None:
- add_end = True
- for l in seg.get_locations("3prime"):
- if l.address == 0 and (l.on_fwd_strand is False):
- add_end = False
- break
- if add_end:
- seg.add_3prime(0,on_fwd_strand=False)
- if seg.end3.connection is None:
- add_end = True
- for l in seg.get_locations("3prime"):
- if l.address == 1 and l.on_fwd_strand:
- add_end = False
- break
- if add_end:
- seg.add_3prime(seg.num_nt-1)
+ five_prime_locs = seg.get_locations("5prime")
+ three_prime_locs = seg.get_locations("3prime")
+
+ 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
+ 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
+
+ if seg.start5.connection is None:
+ if len(list(filter( is_start_5prime, five_prime_locs ))) == 0:
+ seg.add_5prime(0) # TODO ensure this is the same place
+
+ if 'end5' in seg.__dict__ and seg.end5.connection is None:
+ if len(list(filter( is_end_5prime, five_prime_locs ))) == 0:
+ seg.add_5prime(seg.num_nt-1,on_fwd_strand=False)
+
+ if 'start3' in seg.__dict__ and seg.start3.connection is None:
+ if len(list(filter( is_start_3prime, three_prime_locs ))) == 0:
+ seg.add_3prime(0,on_fwd_strand=False)
+
+ if seg.end3.connection is None:
+ if len(list(filter( is_end_3prime, three_prime_locs ))) == 0:
+ seg.add_3prime(seg.num_nt-1)
# print( [(l,l.get_connected_location()) for l in seg.locations] )
# addresses = np.array([l.address for l in seg.get_locations("5prime")])
--
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