def add_fringe(design, fringe_seqs, left_right):
"""Given the design, and fringe sequence, adds the fringe to the design"""
fringe_num = len(fringe_seqs)
if left_right == 'left':
helix_st = 1
else:
helix_st = 0
for i in range(fringe_num):
print(helix_st)
if helix_st == 11:
helix2 = 0
else:
helix2 = helix_st + 1
forward = sc_general.forward_strand(helix_st, 'staple')
forward2 = sc_general.forward_strand(helix2, 'staple')
if forward:
helix = helix_st
else:
helix, helix2 = helix2, helix_st
forward, forward2 = forward2, forward
staple = sc.Strand([sc.Domain(helix = helix, forward = forward, start = 0, end = 16), sc.Domain(helix = helix2, forward = forward2, start = 0, end = 16)], dna_sequence= fringe_seqs[i])
design.add_strand(staple)
helix_st += 2
def add_crossovers(design: sc.Design, crossover_list, scaffold_or_staple):
"""Adds crossovers"""
crossovers = []
for helix in range(len(crossover_list)):
if crossover_list[helix] == 'no crossover':
continue
else:
for crossover in crossover_list[helix]:
helix2 = crossover[1]
offset = crossover[2]
offset2 = crossover[3]
forward = sc_general.forward_strand(helix, scaffold_or_staple)
forward2 = sc_general.forward_strand(helix2, scaffold_or_staple)
crossovers.append(sc.Crossover(helix = helix, helix2 = helix2, offset = offset, offset2 = offset2, forward = forward, forward2 = forward2, half = True))
design.add_crossovers(crossovers)
def add_scaffold_nicks(design: sc.Design, seam_locations):
"""Adds nicks to the precursor scaffold"""
for helix in range(len(seam_locations)):
if seam_locations[helix] == 'no seam':
continue
else:
nick_offsets = seam_locations[helix]
for nick_offset in nick_offsets:
if nick_offset != 'no seam':
forward = sc_general.forward_strand(helix, 'scaffold')
design.add_nick(helix = helix, offset = nick_offset, forward = forward)
def add_adaptor_crossovers(design):
"""Given a adaptor design, adds the crossovers"""
crossovers = []
croosover_locations = [16, 36, 37]
for helix in range(1, 12, 2):
if helix == 11:
helix2 = 0
else:
helix2 = helix + 1
forward = sc_general.forward_strand(helix, 'staple')
forward2 = sc_general.forward_strand(helix2, 'staple')
for offset in croosover_locations:
crossovers.append(
sc.Crossover(helix=helix,
helix2=helix2,
offset=offset,
offset2=offset,
forward=forward,
forward2=forward2,
half=True))
design.add_crossovers(crossovers)
def add_precursor_staples(design: sc.Design, staple_domain, label = None, dna_seq = None):
"""Add precursor staples to the design"""
for helix in range(len(staple_domain)):
if dna_seq == None:
seq = None
else:
seq = dna_seq[helix]
forward = sc_general.forward_strand(helix, 'staple')
outline = staple_domain[helix]
for i in range(outline[0] + 1):
lines = outline[1]
line = lines[i]
start = line[0]
end = line[1]
staples = sc.Strand([sc.Domain(helix = helix, forward = forward, start = start, end = end, label = label)], dna_sequence = seq)
design.add_strand(staples)
def add_precursor_scaffolds(design: sc.Design, shape_outline, label = None, dna_seq = None):
"""Adds the precursor scaffold to the design"""
for helix in range(len(shape_outline)):
if dna_seq == None:
seq = None
else:
seq = dna_seq[helix]
forward = sc_general.forward_strand(helix, 'scaffold')
one_line_outline = shape_outline[helix]
for i in range(one_line_outline[0] + 1):
lines = one_line_outline[1]
line = lines[i]
start = line[0]
end = line[1]
scaffold = sc.Strand([sc.Domain(helix = helix, forward = forward, start = start, end = end, label = label)], dna_sequence = seq, name = 'scaffold')
design.add_strand(scaffold)
def add_staple_nicks(design: sc.Design, nick_locations):
"""Adds nicks ot the precursor staple strands"""
for helix in range(len(nick_locations)):
forward = sc_general.forward_strand(helix, 'staple')
for nick in nick_locations[helix]:
design.add_nick(helix = helix, offset = nick, forward = forward)
def add_hairpins(design, hairpin_locations, hairpin_lattice):
"""Given the design, the hairpin lattice, and the hairpin locations, adds the hairpins to the hairpin lattice and crossovers to the seed"""
seed_domain = range(len(hairpin_locations))
hairpin_domain = range(len(hairpin_locations),
len(hairpin_locations) + len(hairpin_lattice))
#creates the hairpins, included the loopout crossover
for i in range(len(hairpin_domain)):
helix = hairpin_domain[i]
for j in range(len(hairpin_locations[helix - len(seed_domain)])):
left_offset = hairpin_locations[helix - len(seed_domain)][j]
right_offset = left_offset + 8
index = 6 * (i - 1) + j
pin_seq = non_random_hairpin_sequence(index)
staple = sc.Strand([
sc.Domain(helix=helix,
forward=True,
start=left_offset,
end=right_offset),
sc.Loopout(length=4),
sc.Domain(helix=helix,
forward=False,
start=left_offset - 2,
end=right_offset)
],
dna_sequence=pin_seq)
design.add_strand(staple)
#add nicks on staple strands to be able to connect the hairpins
for helix in seed_domain:
forward = sc_general.forward_strand(helix, 'staple')
for nick in hairpin_locations[helix]:
design.add_nick(helix=helix, offset=nick, forward=forward)
#crossovers between the main helices and the hairpins
crossovers = []
for helix in seed_domain:
helix2 = hairpin_domain[helix]
forward = sc_general.forward_strand(helix, 'staple')
for pin in hairpin_locations[helix]:
if forward == True:
forward_pin_offset = pin - 1
reverse_pin_offset = pin
else:
forward_pin_offset = pin
reverse_pin_offset = pin - 1
crossovers.append(
sc.Crossover(helix=helix,
helix2=helix2,
offset=forward_pin_offset,
offset2=pin,
forward=forward,
forward2=True,
half=True))
crossovers.append(
sc.Crossover(helix=helix,
helix2=helix2,
offset=reverse_pin_offset,
offset2=pin - 2,
forward=forward,
forward2=False,
half=True))
design.add_crossovers(crossovers)
seq = seq + sc_adaptor.tile_adapt_seq(helix)
else:
seq = sc_adaptor.tile_adapt_seq(helix) + seq
staple_seq.append(seq)
#scaffold
design = sc_create.create_helices(lattice_domain, lattice, grid_type)
not_fixed_scaf_seq = sc_adaptor.outside_adaptor_seq(sticky_seq)
scaf_seq = []
for helix in range(len(not_fixed_scaf_seq)):
seq = not_fixed_scaf_seq[helix]
if helix % 2 == 1:
seq = seq[5:]
scaf_seq.append(seq)
sc_create.add_precursor_scaffolds(design,
scaffold_domain,
dna_seq=scaf_seq)
#staples
sc_create.add_precursor_staples(design, staple_domain, dna_seq=staple_seq)
for helix in range(1, 12, 2):
forward = sc_general.forward_strand(helix, 'staple')
design.add_nick(helix=helix, offset=24, forward=forward)
for helix in range(12):
forward = sc_general.forward_strand(helix, 'staple')
design.add_nick(helix=helix, offset=37, forward=forward)
sc_adaptor.add_adaptor_crossovers(design)
design.write_scadnano_file()