From 28d4d2776fc1e65d3665f00540605360719673fd Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Wed, 11 Mar 2020 11:38:41 -0500
Subject: [PATCH] Updated routines for removing DNA to optionally allow
removing locations as well
---
mrdna/segmentmodel.py | 77 +++++++++++++++++++++++++++++++++++--------
1 file changed, 63 insertions(+), 14 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 99315a5..f758df5 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -66,9 +66,6 @@ class Location():
self.connection = None
self.is_3prime_side_of_connection = None
- self.prev_in_strand = None
- self.next_in_strand = None
-
self.combine = None # some locations might be combined in bead model
def get_connected_location(self):
@@ -93,6 +90,12 @@ class Location():
raise
return pos
+ def delete(self):
+ if self.connection is not None:
+ self.connection.delete()
+ if self.container is not None:
+ self.container.locations.remove(self)
+
def __repr__(self):
if self.on_fwd_strand:
on_fwd = "on_fwd_strand"
@@ -515,7 +518,7 @@ class Segment(ConnectableElement, Group):
for l,p in zip(self.locations, new_nt_positions):
l.address = self.nt_pos_to_contour(p)
- def remove_dna(self, first_nt: int, last_nt: int):
+ def remove_dna(self, first_nt:int, last_nt:int, remove_locations:bool = False):
""" Removes nucleotides between first_nt and last_nt, inclusive """
assert(np.isclose(np.around(first_nt),first_nt))
assert(np.isclose(np.around(last_nt),last_nt))
@@ -530,28 +533,69 @@ class Segment(ConnectableElement, Group):
if first_nt == last_nt:
return
+ def _transform_contour_positions(contours):
+ nt = self.contour_to_nt_pos(contours)
+ first = first_nt if first_nt > 0 else -np.inf
+ last = last_nt if last_nt < self.num_nt-1 else np.inf
+ bad_ids = (nt >= first) * (nt <= last)
+ nt[nt>last] = nt[nt>last]-removed_nt
+ nt[bad_ids] = np.nan
+ return self.nt_pos_to_contour(nt)* self.num_nt/num_nt
+
first_nt = np.around(first_nt)
last_nt = np.around(last_nt)
- nt_positions = self._get_location_positions()
-
- bad_locations = list(filter(lambda p: p >= first_nt and p <= last_nt, nt_positions))
- if len(bad_locations) > 0:
- raise Exception("Attempted to remove DNA containing locations {} from {} between {} and {}".format(bad_locations,self,first_nt,last_nt))
-
removed_nt = last_nt-first_nt+1
- new_nt_positions = [p if p <= last_nt else p-removed_nt for p in nt_positions]
num_nt = self.num_nt-removed_nt
+ c = np.array([l.address for l in self.locations])
+ new_c = _transform_contour_positions(c)
+
+ if np.any(np.isnan(new_c)) and not remove_locations:
+ raise Exception("Attempted to remove DNA containing locations from {} between {} and {}".format(self,first_nt,last_nt))
+
+ for l,v in zip(list(self.locations),new_c):
+ if np.isnan(v):
+ l.delete()
+ else:
+ l.address = v
+
+ assert( len(self.locations) == np.logical_not(np.isnan(new_c)).sum() )
+ tmp_nt = np.array([l.address*num_nt+0.5 for l in self.locations])
+ assert(np.all( (tmp_nt < 1) + (tmp_nt > num_nt-1) + np.isclose((np.round(tmp_nt) - tmp_nt), 0) ))
+
if self.sequence is not None and len(self.sequence) == self.num_nt:
self.sequence = [s for s,i in zip(self.sequence,range(self.num_nt))
if i < first_nt or i > last_nt]
assert( len(self.sequence) == num_nt )
+ ## Rescale splines
+ def _rescale_splines(u, get_coord_function, set_spline_function):
+ new_u = _transform_contour_positions(u)
+ ids = np.logical_not(np.isnan(new_u))
+ new_u = new_u[ids]
+ new_p = get_coord_function(u[ids])
+ set_spline_function( new_u, new_p )
+
+ _rescale_splines(self.position_spline_params[1],
+ self.contour_to_position,
+ self.set_splines)
+
+ if self.quaternion_spline_params is not None:
+ def _contour_to_quaternion(contours):
+ os = [self.contour_to_orientation(c) for c in contours]
+ qs = [quaternion_from_matrix( o ) for o in os]
+ return np.array(qs)
+ _rescale_splines(self.quaternion_spline_params[1],
+ self.contour_to_quaternion,
+ self.set_splines)
+
self.num_nt = num_nt
- for l,p in zip(self.locations, new_nt_positions):
- l.address = self.nt_pos_to_contour(p)
+ def delete(self):
+ for c,loc,other in self.get_connections_and_locations():
+ c.delete()
+ self.parent.segments.remove(self)
def __filter_contours(contours, positions, position_filter, contour_filter):
u = contours
@@ -1763,9 +1807,12 @@ class SegmentModel(ArbdModel):
except:
pass
self.segments.append(newseg)
+ newseg.parent = self
if include_strands:
for s in other.strands:
- self.strands.append(deepcopy(s))
+ newstrand = deepcopy(s)
+ self.strands.append(newstrand)
+ newstrand.parent = self
else:
for s in other.segments:
try:
@@ -1773,9 +1820,11 @@ class SegmentModel(ArbdModel):
except:
pass
self.segments.append(s)
+ s.parent = self
if include_strands:
for s in other.strands:
self.strands.append(s)
+ s.parent = self
self._clear_beads()
def update(self, segment , copy=False):
--
GitLab