def get_overhang_segs(overhang_ds_edges, overhang_ss_edges,
ss_overhang_sequences):
overhang_segs = {}
for index in overhang_ds_edges:
e = overhang_ds_edges[index]
tmp = copy(
(mrdna.DoubleStrandedSegment(name='helix%s' % (index + 100, ),
num_bp=int(e.nBp),
start_position=list(e.nStart_c),
end_position=list(e.nStop_c))))
overhang_segs[e.index] = tmp
ss_overhang_segs = {}
for index in overhang_ss_edges:
e = overhang_ss_edges[index]
if e.out_orientation == 5:
tmp = copy(
(mrdna.SingleStrandedSegment(name='helix%s' % (index + 200, ),
num_nt=int(e.nBp),
start_position=list(e.nStart_c),
end_position=list(e.nStop_c))))
elif e.out_orientation == 3:
tmp = copy((mrdna.SingleStrandedSegment(
name='helix%s' % (index + 200, ),
num_nt=int(e.nBp),
start_position=list(e.nStop_c),
end_position=list(e.nStart_c),
)))
tmp.sequence = ss_overhang_sequences[index]
ss_overhang_segs[e.index] = (tmp)
return (overhang_segs, ss_overhang_segs)
def create_helix(self):
if self.is_dsdna:
self.dna = mrdna.DoubleStrandedSegment(name=self.name,
start_position = self.start_position,
end_position=self.end_position,
num_bp = self.num_bp)
else:
self.dna = mrdna.SingleStrandedSegment(name=self.name,
start_position = self.start_position,
end_position=self.end_position,
num_nt = self.num_bp)
def apply_connection(self,ss_length):
if ss_length == 0:
self.A.helix.connect_end3(self.B.helix.start5 if self.forward_B else self.B.helix.end5, type_ = "terminal_crossover") if self.forward_A else self.A.helix.connect_start3(self.B.helix.start5 if self.forward_B else self.B.helix.end5, type_ ="terminal_crossover")
else:
self.ss = mrdna.SingleStrandedSegment(str(np.random.rand()),
start_position = self.A.nStop_c if self.forward_A else self.A.nStart_c,
stop_position = self.B.nStart_c if self.forward_B else self.B.nStop_c ,
num_nt=ss_length)
self.A.helix.connect_end3(self.ss) if self.forward_A else self.A.helix.connect_start3(self.ss)
self.B.helix.connect_start5(self.ss) if self.forward_B else self.B.helix.connect_end5(self.ss)
def join_spacerless_overhangs(ss_here, c1_positive, c2_positive, overhang_segs,
segs, c1, c2, vertex_index):
single_stranded_dna = []
if ss_here == 0:
if c1_positive:
segs[c1].connect_end3(overhang_segs[vertex_index].start5,
type_="terminal_crossover")
overhang_segs[vertex_index].connect_start5(
segs[c1].end3, type_="terminal_crossover")
else:
segs[c1[::-1]].connect_start3(overhang_segs[vertex_index].start5,
type_="terminal_crossover")
overhang_segs[vertex_index].connect_start5(
segs[c1[::-1]].start3, type_="terminal_crossover")
if c2_positive:
segs[c2].connect_start5(overhang_segs[vertex_index].start3,
type_="terminal_crossover")
overhang_segs[vertex_index].connect_start3(
segs[c2].start5, type_="terminal_crossover")
else:
segs[c2[::-1]].connect_end5(overhang_segs[vertex_index].start3,
type_="terminal_crossover")
overhang_segs[vertex_index].connect_start3(
segs[c2[::-1]].end5, type_="terminal_crossover")
else:
if c1_positive:
ss = copy(
mrdna.SingleStrandedSegment(
"strand%s" % (np.random.randint(0, high=int(1e10)), ),
start_position=segs[c1].end_position,
end_position=overhang_segs[vertex_index].start_position,
num_nt=ss_here))
segs[c1].connect_end3(ss)
overhang_segs[vertex_index].connect_start5(ss)
single_stranded_dna.append(ss)
else:
ss = copy(
mrdna.SingleStrandedSegment(
"strand%s" % (np.random.randint(0, high=int(1e10)), ),
start_position=segs[c1[::-1]].start_position,
end_position=overhang_segs[vertex_index].start_position,
num_nt=ss_here))
segs[c1[::-1]].connect_start3(ss)
overhang_segs[vertex_index].connect_start5(ss)
single_stranded_dna.append(ss)
if c2_positive:
ss = copy(
mrdna.SingleStrandedSegment(
"strand%s" % (np.random.randint(0, high=int(1e10)), ),
start_position=overhang_segs[vertex_index].end_position,
end_position=segs[c2].start_position,
num_nt=ss_here))
overhang_segs[vertex_index].connect_start3(ss)
segs[c2].connect_start5(ss)
single_stranded_dna.append(ss)
else:
ss = copy(
mrdna.SingleStrandedSegment(
"strand%s" % (np.random.randint(0, high=int(1e10)), ),
start_position=segs[c2[::-1]].end_position,
end_position=overhang_segs[vertex_index].start_position,
num_nt=ss_here))
overhang_segs[vertex_index].connect_start3(ss)
segs[c2[::-1]].connect_end5(ss)
single_stranded_dna.append(ss)
return single_stranded_dna
def join_segments(c1_positive, c2_positive, segs, c1, c2, ssDNA_index,
SPACERS):
single_stranded_dna = []
if SPACERS != 0:
r1 = np.random.rand(1)[0] - 0.5
r2 = np.random.rand(1)[0] - 0.5
if c1_positive and c2_positive:
ss = copy(
mrdna.SingleStrandedSegment(
"strand%s" % (ssDNA_index, ),
start_position=segs[c1].end_position + r1,
end_position=segs[c2].start_position + r2,
num_nt=SPACERS))
segs[c1].connect_end3(ss)
segs[c2].connect_start5(ss)
elif c1_positive and not c2_positive:
ss = copy(
mrdna.SingleStrandedSegment(
"strand%s" % (ssDNA_index, ),
start_position=segs[c1].end_position + r1,
end_position=segs[c2[::-1]].end_position + r2,
num_nt=SPACERS))
segs[c1].connect_end3(ss)
segs[c2[::-1]].connect_end5(ss)
elif not c1_positive and c2_positive:
ss = copy(
mrdna.SingleStrandedSegment(
"strand%s" % (ssDNA_index, ),
start_position=segs[c1[::-1]].start_position + r1,
end_position=segs[c2].start_position + r2,
num_nt=SPACERS))
segs[c1[::-1]].connect_start3(ss)
segs[c2].connect_start5(ss)
elif not c1_positive and not c2_positive:
ss = copy(
mrdna.SingleStrandedSegment(
"strand%s" % (ssDNA_index, ),
start_position=segs[c1[::-1]].start_position + r1,
end_position=segs[c2[::-1]].end_position + r2,
num_nt=SPACERS))
segs[c1[::-1]].connect_start3(ss)
segs[c2[::-1]].connect_end5(ss)
single_stranded_dna.append(ss)
else:
if c1_positive and c2_positive:
segs[c1].connect_end3(segs[c2].start5, type_="terminal_crossover")
elif c1_positive and not c2_positive:
segs[c1].connect_end3(segs[c2[::-1]].end5,
type_="terminal_crossover")
elif not c1_positive and c2_positive:
segs[c1[::-1]].connect_start3(segs[c2].start5,
type_="terminal_crossover")
elif not c1_positive and not c2_positive:
segs[c1[::-1]].connect_start3(segs[c2[::-1]].end5,
type_="terminal_crossover")
return single_stranded_dna
def get_segments(FNAME, LENGTH_OF_SMALLEST, SPACERS,nicks=1,overhangs = None):
locs,faces = read_ply(FNAME)
mentioned_edges = set()
face_data = []
for index,i in enumerate(faces):
print (FACE)
face_data.append(FACE(i,index))
#NICKS
#now we work out where the nicks are so we can choose the correct orientation of our strands.
assign_nicks(face_data)
nick_locs = []
for f in face_data:
nick_locs.append(f.nick)
mentioned_edges = set(nick_locs)
#NICKS
#choose orientation
for i in face_data:
for e in i.e:
if e not in mentioned_edges and e[::-1] not in mentioned_edges:
i.ori.append(1)
mentioned_edges.add(e)
else:
i.ori.append(-1)
edges = []
for i in mentioned_edges:
edges.append(
edge(i,locs[i[0]],locs[i[1]])
)
min_length = np.min([x.rawlen for x in edges])
max_length = np.max([x.rawlen for x in edges])
#ds overhangs
#rework this data structure...
if overhangs is not None:
#overhang_ss_edges_sequences = list(overhangs['ss_seq'])
ss_overhang_sequences = {}
overhang_ds_edges = {}
overhang_ss_edges = {}
for i in range(len(overhangs)):
vertex = overhangs.iloc[i]['overhang']
vertex_location = locs[vertex]
bp = overhangs.iloc[i]['ds_length']
length = bp * min_length / float(LENGTH_OF_SMALLEST) / 3.4
end = length * np.array(vertex_location) / np.sqrt(np.sum(np.array(vertex_location)**2)) + np.array(vertex_location)
overhang_ds_edges[vertex] = edge(vertex,vertex_location,end,overhang=True,bp_overhang=bp)
#ss overhangs
bp_ss = overhangs.iloc[i]['ss_length']
length_ss = bp_ss * min_length / float(LENGTH_OF_SMALLEST) / 3.4
start_ss = end
end_ss = end + length_ss * np.array(vertex_location) / np.sqrt(np.sum(np.array(vertex_location)**2))
overhang_ss_edges[vertex] = edge(vertex,start_ss,end_ss,overhang=True,bp_overhang=bp_ss,out_orientation=overhangs.iloc[i]['out_side'])
ss_overhang_sequences[vertex] = overhangs.iloc[i]['ss_seq']
for i in edges + list(overhang_ds_edges.values()) + list(overhang_ss_edges.values()):
i.normalize(min_length,LENGTH_OF_SMALLEST)
else:
for i in edges:
i.normalize(min_length,LENGTH_OF_SMALLEST)
single_stranded_dna = []
segs = {}
for index, e in enumerate(edges):
segs[tuple(e.index)] = (
mrdna.DoubleStrandedSegment(name = 'helix%s'%(index,),
num_bp = e.nBp,
start_position = e.nStart_c,
end_position = e.nStop_c
))
if overhangs is not None:
#overhangs
overhang_segs = {}
for index in overhang_ds_edges:
e = overhang_ds_edges[index]
tmp = copy((mrdna.DoubleStrandedSegment(name = 'helix%s'%(index+100,),
num_bp = int(e.nBp),
start_position = list(e.nStart_c),
end_position = list(e.nStop_c)
)))
overhang_segs[e.index] = tmp
#overhangs
ss_overhang_segs = {}
for index in overhang_ss_edges:
e = overhang_ss_edges[index]
if e.out_orientation == 5:
tmp = copy((mrdna.SingleStrandedSegment(name = 'helix%s'%(index+200,),
num_nt = int(e.nBp),
start_position = list(e.nStart_c),
end_position = list(e.nStop_c)
)))
elif e.out_orientation == 3:
tmp = copy((mrdna.SingleStrandedSegment(name = 'helix%s'%(index+200,),
num_nt = int(e.nBp),
start_position = list(e.nStop_c),
end_position = list(e.nStart_c),
)))
else:
print ('BUG')
#tmp.sequence = overhangs.iloc[index]['ss_seq']
tmp.sequence = ss_overhang_sequences[index]
#APPLY SEQUENCE HERE USING THE NEW DATA STRUCTURE
print (tmp.sequence)
ss_overhang_segs[e.index]= (tmp)
ssDNA_index = 0
if overhangs is not None:
#CONNECT SS_DNA TO OVERHANGS
for index in overhang_ss_edges:
#connected if they have the same index!
ss = overhang_ss_edges[index]
if overhangs is not None:
dsseg = overhang_segs[index]
ssseg = ss_overhang_segs[index]
#the dsDNA faces outwards
if overhang_ss_edges[index].out_orientation == 3:
overhang_segs[index].connect_end3(ss_overhang_segs[index])
elif overhang_ss_edges[index].out_orientation == 5:
overhang_segs[index].connect_end5(ss_overhang_segs[index])
def intersection(lst1, lst2):
lst3 = [value for value in lst1 if value in lst2]
return lst3
for f in face_data:
for con in f.connections:
### See if we have an overhang
overhang_here = False
if overhangs is not None:
vertex_index = intersection(con[0],con[1])[0]
face_index = f.index
for i in range(len(overhangs)):
if (overhangs.iloc[i]['face'] == face_index and overhangs.iloc[i]['overhang'] == vertex_index):
overhang_here = True
ss_here = overhangs.iloc[i]['ss_extra']
###
if overhang_here:
print (f.index)
ssDNA_index += 1
c1,c2 = con
c1_positive = c1 in segs
c2_positive = c2 in segs
if SPACERS != 0:
if overhang_here:
#TODO : TIDAY ALL OF THIS UP!
if ss_here == 0:
print ('adding overhang here without ss!')
if c1_positive:
segs[c1].connect_end3(overhang_segs[vertex_index].start5, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start5(segs[c1].end3, type_="terminal_crossover")
else:
segs[c1[::-1]].connect_start3(overhang_segs[vertex_index].start5, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start5(segs[c1[::-1]].start3, type_="terminal_crossover")
if c2_positive:
segs[c2].connect_start5(overhang_segs[vertex_index].start3, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start3(segs[c2].start5, type_="terminal_crossover")
else:
segs[c2[::-1]].connect_end5(overhang_segs[vertex_index].start3, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start3(segs[c2[::-1]].end5, type_="terminal_crossover")
else:
# add the connectivity here!
print ('adding overhang here with spacers = %s!'%(ss_here,))
print (ss_here)
if c1_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(np.random.randint(0,high = int(1e10)),),
start_position = segs[c1].end_position ,
end_position = overhang_segs[vertex_index].start_position,
num_nt = ss_here))
segs[c1].connect_end3(ss)
overhang_segs[vertex_index].connect_start5(ss)
single_stranded_dna.append(ss)
else:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(np.random.randint(0,high = int(1e10)),),
start_position = segs[c1[::-1]].start_position ,
end_position = overhang_segs[vertex_index].start_position,
num_nt = ss_here))
segs[c1[::-1]].connect_start3(ss)
overhang_segs[vertex_index].connect_start5(ss)
single_stranded_dna.append(ss)
if c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(np.random.randint(0,high = int(1e10)),),
start_position = overhang_segs[vertex_index].end_position ,
end_position = segs[c2].start_position,
num_nt = ss_here))
overhang_segs[vertex_index].connect_start3(ss)
segs[c2].connect_start5(ss)
single_stranded_dna.append(ss)
else:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(np.random.randint(0,high = int(1e10)),),
start_position = segs[c2[::-1]].end_position ,
end_position = overhang_segs[vertex_index].start_position,
num_nt = ss_here))
overhang_segs[vertex_index].connect_start3(ss)
segs[c2[::-1]].connect_end5(ss)
single_stranded_dna.append(ss)
else:
r1 = np.random.rand(1)[0] - 0.5
r2 = np.random.rand(1)[0] - 0.5
if c1_positive and c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(ssDNA_index,),
start_position = segs[c1].end_position + r1,
end_position = segs[c2].start_position + r2,
num_nt = SPACERS))
segs[c1].connect_end3(ss)
segs[c2].connect_start5(ss)
elif c1_positive and not c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(ssDNA_index,),
start_position = segs[c1].end_position + r1,
end_position = segs[c2[::-1]].end_position + r2,
num_nt = SPACERS))
segs[c1].connect_end3(ss)
segs[c2[::-1]].connect_end5(ss)
elif not c1_positive and c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(ssDNA_index,),
start_position = segs[c1[::-1]].start_position +r1,
end_position = segs[c2].start_position + r2,
num_nt = SPACERS))
segs[c1[::-1]].connect_start3(ss)
segs[c2].connect_start5(ss)
elif not c1_positive and not c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(ssDNA_index,),
start_position = segs[c1[::-1]].start_position +r1 ,
end_position = segs[c2[::-1]].end_position + r2,
num_nt = SPACERS))
segs[c1[::-1]].connect_start3(ss)
segs[c2[::-1]].connect_end5(ss)
single_stranded_dna.append(ss)
else:
#let's also add connectivity to the appropriate overhang...
if overhang_here:
#TODO: need to add additional spacers here!
if ss_here == 0:
if c1_positive:
segs[c1].connect_end3(overhang_segs[vertex_index].start5, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start5(segs[c1].end3, type_="terminal_crossover")
else:
segs[c1[::-1]].connect_start3(overhang_segs[vertex_index].start5, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start5(segs[c1[::-1]].start3, type_="terminal_crossover")
if c2_positive:
segs[c2].connect_start5(overhang_segs[vertex_index].start3, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start3(segs[c2].start5, type_="terminal_crossover")
else:
segs[c2[::-1]].connect_end5(overhang_segs[vertex_index].start3, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start3(segs[c2[::-1]].end5, type_="terminal_crossover")
else:
if c1_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(np.random.randint(0,high = int(1e10)),),
start_position = segs[c1].end_position ,
end_position = overhang_segs[vertex_index].start_position,
num_nt = ss_here))
segs[c1].connect_end3(ss)
overhang_segs[vertex_index].connect_start5(ss)
single_stranded_dna.append(ss)
else:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(np.random.randint(0,high = int(1e10)),),
start_position = segs[c1[::-1]].start_position ,
end_position = overhang_segs[vertex_index].start_position,
num_nt = ss_here))
segs[c1[::-1]].connect_start3(ss)
overhang_segs[vertex_index].connect_start5(ss)
single_stranded_dna.append(ss)
if c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(np.random.randint(0,high = int(1e10)),),
start_position = overhang_segs[vertex_index].end_position ,
end_position = segs[c2].start_position,
num_nt = ss_here))
overhang_segs[vertex_index].connect_start3(ss)
segs[c2].connect_start5(ss)
single_stranded_dna.append(ss)
else:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(np.random.randint(0,high = int(1e10)),),
start_position = segs[c2[::-1]].end_position ,
end_position = overhang_segs[vertex_index].start_position,
num_nt = ss_here))
overhang_segs[vertex_index].connect_start3(ss)
segs[c2[::-1]].connect_end5(ss)
single_stranded_dna.append(ss)
if not overhang_here:
if c1_positive and c2_positive:
segs[c1].connect_end3(segs[c2].start5, type_="terminal_crossover")
elif c1_positive and not c2_positive:
segs[c1].connect_end3(segs[c2[::-1]].end5, type_="terminal_crossover")
elif not c1_positive and c2_positive:
segs[c1[::-1]].connect_start3(segs[c2].start5, type_="terminal_crossover")
elif not c1_positive and not c2_positive:
segs[c1[::-1]].connect_start3(segs[c2[::-1]].end5, type_="terminal_crossover")
#NICKS
#TODO: just have nicks on non-overhang sides!!!
#the list of faces which correspond to overhangs should be accessible no?
no_nick_faces = []
if type(overhangs) != type(None):
#if overhangs != None:
no_nick_faces = list(overhangs['face'])
if nicks:
print ("adding nicks!")
for f in face_data:
nick = f.nick
if ((nick in segs) and (f.index not in no_nick_faces)):
segs[nick].add_nick(10,on_fwd_strand=True)
else:
print ('failure')
#make sure that all the ssDNA has the sequence 'TTT...'
for s in single_stranded_dna:
s.sequence = s.num_nt * 'T'
if overhangs is not None:
segs_list = [segs[i] for i in segs] + single_stranded_dna + [overhang_segs[i] for i in overhang_segs] + [ss_overhang_segs[i] for i in ss_overhang_segs]
else:
segs_list = [segs[i] for i in segs] + single_stranded_dna
return segs_list
def get_segments(FNAME, LENGTH_OF_SMALLEST, SPACERS):
locs,faces = read_ply(FNAME)
mentioned_edges = set()
face_data = [face(i) for i in faces]
for i in face_data:
for e in i.e:
if e not in mentioned_edges and e[::-1] not in mentioned_edges:
i.ori.append(1)
mentioned_edges.add(e)
else:
i.ori.append(-1)
edges = []
for i in mentioned_edges:
edges.append(
edge(i,locs[i[0]],locs[i[1]])
)
min_length = np.min([x.rawlen for x in edges])
max_length = np.max([x.rawlen for x in edges])
for i in edges:
i.normalize(min_length,LENGTH_OF_SMALLEST)
single_stranded_dna = []
segs = {}
for index, e in enumerate(edges):
segs[tuple(e.index)] = (
mrdna.DoubleStrandedSegment(name = 'helix%s'%(index,),
num_bp = e.nBp,
start_position = e.nStart_c,
end_position = e.nStop_c
))
ssDNA_index = 0
for f in face_data:
for con in f.connections:
ssDNA_index += 1
c1,c2 = con
c1_positive = c1 in segs
c2_positive = c2 in segs
if c1_positive and c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(ssDNA_index,),
start_position = segs[c1].end_position ,
end_position = segs[c2].start_position,
num_nt = SPACERS))
segs[c1].connect_end3(ss)
segs[c2].connect_start5(ss)
elif c1_positive and not c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(ssDNA_index,),
start_position = segs[c1].end_position ,
end_position = segs[c2[::-1]].end_position,
num_nt = SPACERS))
segs[c1].connect_end3(ss)
segs[c2[::-1]].connect_end5(ss)
elif not c1_positive and c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(ssDNA_index,),
start_position = segs[c1[::-1]].start_position ,
end_position = segs[c2].start_position,
num_nt = SPACERS))
segs[c1[::-1]].connect_start3(ss)
segs[c2].connect_start5(ss)
elif not c1_positive and not c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(ssDNA_index,),
start_position = segs[c1[::-1]].start_position ,
end_position = segs[c2[::-1]].end_position,
num_nt = SPACERS))
#segs[c1[::-1]].connect_start3(segs[c2[::-1]].end5)
segs[c1[::-1]].connect_start3(ss)
segs[c2[::-1]].connect_end5(ss)
single_stranded_dna.append(ss)
'''
if c1_positive and c2_positive:
segs[c1].connect_end3(segs[c2].start5)
elif c1_positive and not c2_positive:
segs[c1].connect_end3(segs[c2[::-1]].end5)
elif not c1_positive and c2_positive:
segs[c1[::-1]].connect_start3(segs[c2].start5)
elif not c1_positive and not c2_positive:
segs[c1[::-1]].connect_start3(segs[c2[::-1]].end5)
else:
print ('ohfuck')
'''
#todo: add terminal crossovers to allow 0 free ssDNA.
segs_list = [segs[i] for i in segs] + single_stranded_dna
return segs_list
def get_segments(FNAME, LENGTH_OF_SMALLEST, SPACERS,overhangs = None):
locs,faces = read_ply(FNAME)
mentioned_edges = set()
face_data = []
for index,i in enumerate(faces):
print (FACE)
face_data.append(FACE(i,index))
#NICKS
#now we work out where the nicks are so we can choose the correct orientation of our strands.
assign_nicks(face_data)
nick_locs = []
for f in face_data:
nick_locs.append(f.nick)
mentioned_edges = set(nick_locs)
#NICKS
#choose orientation
for i in face_data:
for e in i.e:
if e not in mentioned_edges and e[::-1] not in mentioned_edges:
i.ori.append(1)
mentioned_edges.add(e)
else:
i.ori.append(-1)
edges = []
for i in mentioned_edges:
edges.append(
edge(i,locs[i[0]],locs[i[1]])
)
min_length = np.min([x.rawlen for x in edges])
max_length = np.max([x.rawlen for x in edges])
#ds overhangs
#rework this data structure...
if overhangs is not None:
overhang_ds_edges = []
overhang_ss_edges = []
for i in range(len(overhangs)):
vertex = overhangs.iloc[i]['overhang']
vertex_location = locs[vertex]
##ds overhangs
bp = overhangs.iloc[i]['ds_length']
length = bp * min_length / float(LENGTH_OF_SMALLEST) / 3.4
end = length * np.array(vertex_location) / np.sqrt(np.sum(np.array(vertex_location)**2)) + np.array(vertex_location)
overhang_ds_edges.append(edge(vertex,vertex_location,end,overhang=True,bp_overhang=bp))
#ss overhangs
bp_ss = overhangs.iloc[i]['ss_length']
length_ss = bp_ss * min_length / float(LENGTH_OF_SMALLEST) / 3.4
start_ss = end
end_ss = end + length_ss * np.array(vertex_location) / np.sqrt(np.sum(np.array(vertex_location)**2))
overhang_ss_edges.append(edge(vertex,start_ss,end_ss,overhang=True,bp_overhang=bp_ss,out_orientation=overhangs.iloc[i]['out_side']))
for i in edges + overhang_ds_edges + overhang_ss_edges:
i.normalize(min_length,LENGTH_OF_SMALLEST)
else:
for i in edges:
i.normalize(min_length,LENGTH_OF_SMALLEST)
single_stranded_dna = []
segs = {}
for index, e in enumerate(edges):
segs[tuple(e.index)] = (
mrdna.DoubleStrandedSegment(name = 'helix%s'%(index,),
num_bp = e.nBp,
start_position = e.nStart_c,
end_position = e.nStop_c
))
if overhangs is not None:
#overhangs
overhang_segs = {}
for index, e in enumerate(overhang_ds_edges):
tmp = copy((mrdna.DoubleStrandedSegment(name = 'helix%s'%(index+100,),
num_bp = int(e.nBp),
start_position = list(e.nStart_c),
end_position = list(e.nStop_c)
)))
overhang_segs[e.index] = tmp
#overhangs
ss_overhang_segs = {}
for index, e in enumerate(overhang_ss_edges):
if e.out_orientation == 5:
tmp = copy((mrdna.SingleStrandedSegment(name = 'helix%s'%(index+200,),
num_nt = int(e.nBp),
start_position = list(e.nStart_c),
end_position = list(e.nStop_c)
)))
elif e.out_orientation == 3:
tmp = copy((mrdna.SingleStrandedSegment(name = 'helix%s'%(index,),
num_nt = int(e.nBp),
start_position = list(e.nStop_c),
end_position = list(e.nStart_c),
)))
else:
print ('BUG')
ss_overhang_segs[e.index]= (tmp)
ssDNA_index = 0
if overhangs is not None:
#CONNECT SS_DNA TO OVERHANGS
for ss in overhang_ss_edges:
#connected if they have the same index!
index = ss.index
if overhangs is not None:
dsseg = overhang_segs[index]
ssseg = ss_overhang_segs[index]
#the dsDNA faces outwards
if overhang_ss_edges[index].out_orientation == 3:
overhang_segs[index].connect_end3(ss_overhang_segs[index])
elif overhang_ss_edges[index].out_orientation == 5:
overhang_segs[index].connect_end5(ss_overhang_segs[index])
def intersection(lst1, lst2):
lst3 = [value for value in lst1 if value in lst2]
return lst3
for f in face_data:
for con in f.connections:
### See if we have an overhang
overhang_here = False
if overhangs is not None:
vertex_index = intersection(con[0],con[1])[0]
face_index = f.index
for i in range(len(overhangs)):
if (overhangs.iloc[i]['face'] == face_index and overhangs.iloc[i]['overhang'] == vertex_index):
overhang_here = True
###
if overhang_here:
print (f.index)
#but obviously there isn't only one overhang?
ssDNA_index += 1
c1,c2 = con
c1_positive = c1 in segs
c2_positive = c2 in segs
if SPACERS != 0:
if overhang_here:
print ('adding overhang here!')
if c1_positive:
segs[c1].connect_end3(overhang_segs[vertex_index].start5, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start5(segs[c1].end3, type_="terminal_crossover")
else:
segs[c1[::-1]].connect_start3(overhang_segs[vertex_index].start5, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start5(segs[c1[::-1]].start3, type_="terminal_crossover")
if c2_positive:
segs[c2].connect_start5(overhang_segs[vertex_index].start3, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start3(segs[c2].start5, type_="terminal_crossover")
else:
segs[c2[::-1]].connect_end5(overhang_segs[vertex_index].start3, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start3(segs[c2[::-1]].end5, type_="terminal_crossover")
else:
if c1_positive and c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(ssDNA_index,),
start_position = segs[c1].end_position ,
end_position = segs[c2].start_position,
num_nt = SPACERS))
segs[c1].connect_end3(ss)
segs[c2].connect_start5(ss)
elif c1_positive and not c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(ssDNA_index,),
start_position = segs[c1].end_position ,
end_position = segs[c2[::-1]].end_position,
num_nt = SPACERS))
segs[c1].connect_end3(ss)
segs[c2[::-1]].connect_end5(ss)
elif not c1_positive and c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(ssDNA_index,),
start_position = segs[c1[::-1]].start_position ,
end_position = segs[c2].start_position,
num_nt = SPACERS))
segs[c1[::-1]].connect_start3(ss)
segs[c2].connect_start5(ss)
elif not c1_positive and not c2_positive:
ss = copy(mrdna.SingleStrandedSegment("strand%s"%(ssDNA_index,),
start_position = segs[c1[::-1]].start_position ,
end_position = segs[c2[::-1]].end_position,
num_nt = SPACERS))
#segs[c1[::-1]].connect_start3(segs[c2[::-1]].end5)
segs[c1[::-1]].connect_start3(ss)
segs[c2[::-1]].connect_end5(ss)
single_stranded_dna.append(ss)
else:
#let's also add connectivity to the appropriate overhang...
if overhang_here:
if c1_positive:
segs[c1].connect_end3(overhang_segs[vertex_index].start5, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start5(segs[c1].end3, type_="terminal_crossover")
else:
segs[c1[::-1]].connect_start3(overhang_segs[vertex_index].start5, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start5(segs[c1[::-1]].start3, type_="terminal_crossover")
if c2_positive:
segs[c2].connect_start5(overhang_segs[vertex_index].start3, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start3(segs[c2].start5, type_="terminal_crossover")
else:
segs[c2[::-1]].connect_end5(overhang_segs[vertex_index].start3, type_="terminal_crossover")
overhang_segs[vertex_index].connect_start3(segs[c2[::-1]].end5, type_="terminal_crossover")
if not overhang_here:
if c1_positive and c2_positive:
segs[c1].connect_end3(segs[c2].start5, type_="terminal_crossover")
elif c1_positive and not c2_positive:
segs[c1].connect_end3(segs[c2[::-1]].end5, type_="terminal_crossover")
elif not c1_positive and c2_positive:
segs[c1[::-1]].connect_start3(segs[c2].start5, type_="terminal_crossover")
elif not c1_positive and not c2_positive:
segs[c1[::-1]].connect_start3(segs[c2[::-1]].end5, type_="terminal_crossover")
#NICKS
nicks = False
if nicks == True:
for f in face_data:
nick = f.nick
if nick in segs:
segs[nick].add_nick(10,on_fwd_strand=True)
else:
print ('failure')
if overhangs is not None:
segs_list = [segs[i] for i in segs] + single_stranded_dna + [overhang_segs[i] for i in overhang_segs] + [ss_overhang_segs[i] for i in ss_overhang_segs]
else:
segs_list = [segs[i] for i in segs] + single_stranded_dna
return segs_list
def get_segments(FNAME, LENGTH_OF_SMALLEST, SPACERS):
locs, faces = read_ply(FNAME)
mentioned_edges = set()
face_data = [face(i) for i in faces]
#NICKS
#now we work out where the nicks are so we can choose the correct orientation of our strands.
assign_nicks(face_data)
nick_locs = []
for f in face_data:
nick_locs.append(f.nick)
mentioned_edges = set(nick_locs)
#NICKS
for i in face_data:
for e in i.e:
if e not in mentioned_edges and e[::-1] not in mentioned_edges:
i.ori.append(1)
mentioned_edges.add(e)
else:
i.ori.append(-1)
edges = []
for i in mentioned_edges:
edges.append(edge(i, locs[i[0]], locs[i[1]]))
min_length = np.min([x.rawlen for x in edges])
max_length = np.max([x.rawlen for x in edges])
for i in edges:
i.normalize(min_length, LENGTH_OF_SMALLEST)
single_stranded_dna = []
segs = {}
for index, e in enumerate(edges):
segs[tuple(e.index)] = (mrdna.DoubleStrandedSegment(
name='helix%s' % (index, ),
num_bp=e.nBp,
start_position=e.nStart_c,
end_position=e.nStop_c))
ssDNA_index = 0
for f in face_data:
for con in f.connections:
ssDNA_index += 1
c1, c2 = con
c1_positive = c1 in segs
c2_positive = c2 in segs
if SPACERS != 0:
if c1_positive and c2_positive:
ss = copy(
mrdna.SingleStrandedSegment(
"strand%s" % (ssDNA_index, ),
start_position=segs[c1].end_position,
end_position=segs[c2].start_position,
num_nt=SPACERS))
segs[c1].connect_end3(ss)
segs[c2].connect_start5(ss)
elif c1_positive and not c2_positive:
ss = copy(
mrdna.SingleStrandedSegment(
"strand%s" % (ssDNA_index, ),
start_position=segs[c1].end_position,
end_position=segs[c2[::-1]].end_position,
num_nt=SPACERS))
segs[c1].connect_end3(ss)
segs[c2[::-1]].connect_end5(ss)
elif not c1_positive and c2_positive:
ss = copy(
mrdna.SingleStrandedSegment(
"strand%s" % (ssDNA_index, ),
start_position=segs[c1[::-1]].start_position,
end_position=segs[c2].start_position,
num_nt=SPACERS))
segs[c1[::-1]].connect_start3(ss)
segs[c2].connect_start5(ss)
elif not c1_positive and not c2_positive:
ss = copy(
mrdna.SingleStrandedSegment(
"strand%s" % (ssDNA_index, ),
start_position=segs[c1[::-1]].start_position,
end_position=segs[c2[::-1]].end_position,
num_nt=SPACERS))
#segs[c1[::-1]].connect_start3(segs[c2[::-1]].end5)
segs[c1[::-1]].connect_start3(ss)
segs[c2[::-1]].connect_end5(ss)
single_stranded_dna.append(ss)
else:
if c1_positive and c2_positive:
segs[c1].connect_end3(segs[c2].start5,
type_="terminal_crossover")
elif c1_positive and not c2_positive:
segs[c1].connect_end3(segs[c2[::-1]].end5,
type_="terminal_crossover")
elif not c1_positive and c2_positive:
segs[c1[::-1]].connect_start3(segs[c2].start5,
type_="terminal_crossover")
elif not c1_positive and not c2_positive:
segs[c1[::-1]].connect_start3(segs[c2[::-1]].end5,
type_="terminal_crossover")
#NICKS
for f in face_data:
nick = f.nick
if nick in segs:
segs[nick].add_nick(5, on_fwd_strand=True)
else:
print('failure')
#
segs_list = [segs[i] for i in segs] + single_stranded_dna
return segs_list