def add_angle_inducing_insertions_deletions(design: sc.Design) -> None:
# insertion followed by deletion
start = 59
end = start + (32 * 12)
for helix in [1, 5, 7, 11, 13]:
for offset in range(start, end, 32):
design.add_insertion(helix, offset, 1)
design.add_deletion(helix, offset + 16)
# deletion followed by insertion
for helix in [2, 4, 8, 10, 14]:
for offset in range(start, end, 32):
design.add_deletion(helix, offset)
design.add_insertion(helix, offset + 16, 1)
def add_domains_for_barrel_seam(design: sc.Design) -> None:
top_staples_5p = design.strands_starting_on_helix(0)
top_staples_3p = design.strands_ending_on_helix(0)
bot_staples_5p = design.strands_starting_on_helix(15)
bot_staples_3p = design.strands_ending_on_helix(15)
# remove scaffold
top_staples_5p = [st for st in top_staples_5p if len(st.domains) <= 3]
top_staples_3p = [st for st in top_staples_3p if len(st.domains) <= 3]
bot_staples_5p = [st for st in bot_staples_5p if len(st.domains) <= 3]
bot_staples_3p = [st for st in bot_staples_3p if len(st.domains) <= 3]
top_staples_5p.sort(key=lambda stap: stap.offset_5p())
top_staples_3p.sort(key=lambda stap: stap.offset_3p())
bot_staples_5p.sort(key=lambda stap: stap.offset_5p())
bot_staples_3p.sort(key=lambda stap: stap.offset_3p())
for top_5p, top_3p, bot_5p, bot_3p in zip(top_staples_5p, top_staples_3p,
bot_staples_5p, bot_staples_3p):
ss_top = sc.Domain(helix=0,
forward=False,
start=top_5p.first_domain().end,
end=top_3p.last_domain().start)
ss_bot = sc.Domain(helix=15,
forward=True,
start=bot_3p.last_domain().end,
end=bot_5p.first_domain().start)
design.insert_domain(bot_5p, 0, ss_top)
design.insert_domain(top_5p, 0, ss_bot)
def add_adapters(design: sc.Design) -> None:
# left adapters
left_inside_seed = 48
left_outside_seed = left_inside_seed - 26
for bot_helix in range(2, 18, 2):
top_helix = bot_helix - 1 if bot_helix != 2 else 17
ss_top = sc.Domain(helix=top_helix,
forward=True,
start=left_outside_seed,
end=left_inside_seed)
ss_bot = sc.Domain(helix=bot_helix,
forward=False,
start=left_outside_seed,
end=left_inside_seed)
idt = sc.IDTFields(name=f'adap-left-{top_helix}-{bot_helix}',
scale='25nm',
purification='STD')
adapter = sc.Strand(domains=[ss_bot, ss_top], idt=idt)
design.add_strand(adapter)
# right adapters
right_inside_seed = 464
right_outside_seed = right_inside_seed + 26
for bot_helix in range(2, 18, 2):
top_helix = bot_helix - 1 if bot_helix != 2 else 17
ss_top = sc.Domain(helix=top_helix,
forward=True,
start=right_inside_seed,
end=right_outside_seed)
ss_bot = sc.Domain(helix=bot_helix,
forward=False,
start=right_inside_seed,
end=right_outside_seed)
idt = sc.IDTFields(name=f'adap-right-{top_helix}-{bot_helix}',
scale='25nm',
purification='STD')
adapter = sc.Strand(domains=[ss_top, ss_bot], idt=idt)
design.add_strand(adapter)
def add_tiles_and_assign_dna(design: sc.Design) -> None:
# left tiles
left_left = 11
left_right = 32
for top_helix, seq in zip(range(2, 18, 2), tile_dna_seqs):
bot_helix = top_helix + 1
ss_top = sc.Domain(helix=top_helix,
forward=True,
start=left_left,
end=left_right)
ss_bot = sc.Domain(helix=bot_helix,
forward=False,
start=left_left,
end=left_right)
idt = sc.IDTFields(name=f'tile-left-{top_helix}-{bot_helix}',
scale='25nm',
purification='STD')
tile = sc.Strand(domains=[ss_bot, ss_top],
color=sc.Color(0, 0, 0),
idt=idt)
design.add_strand(tile)
design.assign_dna(tile, seq)
# right tiles
right_left = 480
right_right = 501
for top_helix, seq in zip(range(2, 18, 2), tile_dna_seqs):
bot_helix = top_helix + 1
ss_top = sc.Domain(helix=top_helix,
forward=True,
start=right_left,
end=right_right)
ss_bot = sc.Domain(helix=bot_helix,
forward=False,
start=right_left,
end=right_right)
idt = sc.IDTFields(name=f'tile-right-{top_helix}-{bot_helix}',
scale='25nm',
purification='STD')
tile = sc.Strand(domains=[ss_bot, ss_top],
color=sc.Color(0, 0, 0),
idt=idt)
design.add_strand(tile)
design.assign_dna(tile, seq)
def move_top_and_bottom_staples_within_column_boundaries(design: sc.Design):
top_staples = design.strands_starting_on_helix(0)
bot_staples = design.strands_starting_on_helix(15)
bot_staples.remove(design.scaffold)
for top_staple in top_staples:
current_end = top_staple.domains[0].end
design.set_end(top_staple.domains[0], current_end - 8)
for bot_staple in bot_staples:
current_start = bot_staple.domains[0].start
design.set_start(bot_staple.domains[0], current_start + 8)
def valid_deletion_offset(design: sc.Design, helix: int, offset: int) -> bool:
domains_at_offset = design.domains_at(helix, offset)
if len(domains_at_offset) > 2:
raise ValueError(f'Invalid Design; more than two Substrands found at '
f'helix {helix} and offset {offset}: '
f'{domains_at_offset}')
elif len(domains_at_offset) != 2:
return False
for ss in domains_at_offset:
if offset in ss.deletions:
return False # already a deletion there
if offset in (insertion[0] for insertion in ss.insertions):
return False # already an insertion there
if offset == ss.start:
return False # no 5' end
if offset == ss.end - 1:
return False # no 3' end
return True
def add_scaffold_crossovers(design: sc.Design) -> None:
for helix in range(1, 23, 2): # scaffold interior crossovers
design.add_full_crossover(helix=helix,
helix2=helix + 1,
offset=144,
forward=False)
for helix in range(0, 23, 2): # scaffold edges crossovers
design.add_half_crossover(helix=helix,
helix2=helix + 1,
offset=0,
forward=True)
design.add_half_crossover(helix=helix,
helix2=helix + 1,
offset=287,
forward=True)
def add_crossovers(design: sc.Design) -> None:
# staples interior
for offset in range(84, 1246, 42):
design.add_full_crossover(helix=0,
helix2=1,
offset=offset,
forward=False)
design.add_full_crossover(helix=3,
helix2=4,
offset=offset,
forward=True)
for offset in range(56, 1246, 42):
design.add_full_crossover(helix=1,
helix2=2,
offset=offset,
forward=True)
design.add_full_crossover(helix=4,
helix2=5,
offset=offset,
forward=False)
for offset in range(70, 1246, 42):
design.add_full_crossover(helix=2,
helix2=3,
offset=offset,
forward=False)
design.add_full_crossover(helix=5,
helix2=0,
offset=offset,
forward=True)
for offset in range(49, 1245,
42): # extra crossovers 5 - 0 for some reason
design.add_full_crossover(helix=5,
helix2=0,
offset=offset,
forward=True)
# staples edges
design.add_half_crossover(helix=0, helix2=1, offset=42, forward=False)
design.add_half_crossover(helix=3, helix2=4, offset=42, forward=True)
design.add_half_crossover(helix=0, helix2=5, offset=1245, forward=False)
design.add_half_crossover(helix=2, helix2=3, offset=1245, forward=False)
# scaffold interior
for offset in range(58, 1250, 42):
design.add_full_crossover(helix=0,
helix2=1,
offset=offset,
forward=True)
for offset in range(30, 1250, 42):
design.add_full_crossover(helix=1,
helix2=2,
offset=offset,
forward=False)
for offset in range(54, 1250, 42):
design.add_full_crossover(helix=2,
helix2=3,
offset=offset,
forward=True)
for offset in range(26, 1250, 42):
design.add_full_crossover(helix=3,
helix2=4,
offset=offset,
forward=False)
# scaffold edges
design.add_half_crossover(helix=0, helix2=1, offset=16, forward=True)
design.add_half_crossover(helix=2, helix2=3, offset=12, forward=True)
design.add_half_crossover(helix=4, helix2=5, offset=19, forward=True)
design.add_half_crossover(helix=0, helix2=1, offset=1275, forward=True)
design.add_half_crossover(helix=2, helix2=3, offset=1271, forward=True)
design.add_half_crossover(helix=4, helix2=5, offset=1278, forward=True)
def add_nicks(design: sc.Design) -> None:
design.add_nick(helix=5, offset=399, forward=False) # scaffold
for offset in range(56, 1246, 42):
design.add_nick(helix=0, offset=offset, forward=False)
design.add_nick(helix=3, offset=offset, forward=True)
for offset in range(70, 1246, 42):
design.add_nick(helix=1, offset=offset, forward=True)
design.add_nick(helix=4, offset=offset, forward=False)
for offset in range(84, 1246, 42):
design.add_nick(helix=2, offset=offset, forward=False)
design.add_nick(helix=5, offset=offset, forward=True)
def add_scaffold_nicks(design: sc.Design):
crossovers = []
for helix in range(3, maxhelix, 2):
if not design.strands_starting_on_helix(helix):
pass
else:
hel1 = helix #first starting helix
break
for helix in range(hel1, maxhelix, 2):
scafdom1 = design.strands_starting_on_helix(helix)
scafdom2 = design.strands_starting_on_helix(helix + 1)
if not (scafdom1
and scafdom2): #check for empty helix at the end of the design
break
imghelix = int((helix - 1) / 2)
if (1 in img[imghelix]) and (1 in img[imghelix + 1]):
interstarts = []
interends = []
for dom in range(1, len(img[imghelix])):
if (bool(img[imghelix][dom] and img[imghelix+1][dom])) and \
(not bool(img[imghelix][dom-1] and img[imghelix+1][dom-1])):
interstarts.append(dom)
if (not bool(img[imghelix][dom] and img[imghelix+1][dom])) and \
(bool(img[imghelix][dom-1] and img[imghelix+1][dom-1])):
interends.append(dom)
interstarts = [x * block for x in interstarts]
interends = [x * block for x in interends]
for i in range(len(interstarts)):
#finds the scaffold crossover offset position 'nickoff', for the square lattice,
#closest to the center of the intersection of helices that are crossing over
closestoff = int((interstarts[i] + interends[i]) / 2) - 2
closerem = (closestoff) % 32
if (closerem < 10):
nickoff = 3 + 32 * int(closestoff / 32)
if nickoff <= interstarts[i]:
nickoff = 3 + 32 * int(closestoff / 32) + 10
elif nickoff >= interends[i]:
nickoff = 3 + 32 * int(closestoff / 32) - 11
elif (closerem > 10) and (closerem < 21):
nickoff = 3 + 32 * int(closestoff / 32) + 10
if nickoff <= interstarts[i]:
nickoff = 3 + 32 * int(closestoff / 32) + 21
elif nickoff >= interends[i]:
nickoff = 3 + 32 * int(closestoff / 32)
elif (closerem > 21) and (closerem < 32):
nickoff = 3 + 32 * int(closestoff / 32) + 21
if nickoff <= interstarts[i]:
nickoff = 3 + 32 * int(closestoff / 32) + 32
elif nickoff >= interends[i]:
nickoff = 3 + 32 * int(closestoff / 32) + 10
else:
nickoff = 3 + 32 * int(closestoff / 32) + closerem
design.add_nick(helix=helix,
offset=nickoff,
forward=helix % 2 == 0)
design.add_nick(helix=helix + 1,
offset=nickoff,
forward=helix % 2 == 1)
crossovers.append(
sc.Crossover(helix=helix,
helix2=helix + 1,
offset=nickoff,
forward=False))
design.add_nick(helix=helix, offset=nickoff, forward=helix % 2 == 0)
design.add_crossovers(crossovers)
def add_staple_nicks(design: sc.Design):
crossovers = []
for helix in range(3, maxhelix, 2):
if not design.strands_starting_on_helix(helix):
pass
else:
hel1 = helix #first starting helix
break
for helix in range(hel1, maxhelix, 2):
scafdom1 = design.strands_starting_on_helix(helix)
scafdom2 = design.strands_starting_on_helix(helix + 1)
if not (scafdom1
and scafdom2): #check for empty helix at the end of the design
break
for helix in range(maxhelix):
if helix % 2 == 0:
for offset in range(block * cmax):
if (offset % 32 == 0) and (design.domains_at(helix, offset)):
if domain_end(design, helix,
offset): #no nick if domain end
continue
#Prevent very short staples
if (design.domains_at(helix, offset-16)) and \
(design.domains_at(helix, offset+16)):
design.add_nick(helix=helix,
offset=offset,
forward=helix % 2 == 1)
if 0<=(offset-8)<=block*cmax and \
(design.domains_at(helix, offset-16)) and \
(design.domains_at(helix, offset)) and \
(design.domains_at(helix+1, offset-8)) and \
(design.domains_at(helix+1, offset-9)) and \
not domain_end(design, helix, offset-8):
crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, \
offset=offset-8, forward=helix % 2 == 1))
else:
for offset in range(block * cmax):
if ((offset + 16) % 32 == 0) and (design.domains_at(
helix, offset)):
if domain_end(design, helix, offset):
continue
#Prevent very short staples
if (design.domains_at(helix, offset-16)) and \
(design.domains_at(helix, offset+16)):
design.add_nick(helix=helix,
offset=offset,
forward=helix % 2 == 1)
if 0<=(offset-8)<=block*cmax and \
(design.domains_at(helix, offset-16)) and \
(design.domains_at(helix, offset)) and \
(design.domains_at(helix+1, offset-8)) and \
(design.domains_at(helix+1, offset-9)) and \
not domain_end(design, helix, offset-8):
crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, \
offset=offset-8, forward=helix % 2 == 1))
design.add_crossovers(crossovers)
def add_staple_nicks(design: sc.Design):
crossovers = []
midgap = 3
state = 0
every = -1 #skip every xth crossover
for helix in range(3, maxhelix, 2):
if not design.strands_starting_on_helix(helix):
pass
else:
hel1 = helix #first starting helix
break
for helix in range(hel1, maxhelix, 2):
scafdom1 = design.strands_starting_on_helix(helix)
scafdom2 = design.strands_starting_on_helix(helix + 1)
if not (scafdom1
and scafdom2): #check for empty helix at the end of the design
break
for helix in range(maxhelix):
if helix % 2 == 0:
for offset in range(block * cmax):
if (((offset-3)%32==0) or \
((offset-3)%32==10) or \
((offset-3)%32==21)) and \
(design.domains_at(helix, offset+midgap)):
state = state + 1
if not every == -1:
if state % every == 0:
# print(str(helix)+' '+str(offset))
continue
if domain_end(design, helix,
offset + midgap): #no nick if domain end
continue
#Prevent very short staples
if long_stap_cond(design, helix, offset + midgap) == True:
design.add_nick(helix=helix,
offset=offset + midgap,
forward=helix % 2 == 1)
if cross_conds(design, helix, offset):
crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, \
offset=offset, forward=helix % 2 == 1))
elif helix == 2:
print("not here " + str(offset))
else:
for offset in range(block * cmax):
if (((offset-8)%32==0) or \
((offset-8)%32==11) or \
((offset-8)%32==21)) and \
(design.domains_at(helix, offset+midgap)):
state = state + 1
if not every == -1:
if state % every == 0:
# print(str(helix)+' '+str(offset))
continue
if domain_end(design, helix,
offset + midgap): #no nick if domain end
continue
# #Prevent very short staples
# if long_stap_cond(design, helix, offset+midgap)==True:
# design.add_nick(helix=helix, offset=offset+midgap, forward=helix % 2 == 1)
if cross_conds(design, helix, offset):
crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, \
offset=offset, forward=helix % 2 == 1))
design.add_crossovers(crossovers)
def add_scaffold_nicks(design: sc.Design):
for helix in range(1, 24):
design.add_nick(helix=helix, offset=152, forward=helix % 2 == 0)
def add_deletions(design: sc.Design):
for helix in range(24):
for offset in range(27, 294, 48):
design.add_deletion(helix, offset)
def add_staple_nicks(design: sc.Design):
for helix in range(24):
start_offset = 32 if helix % 2 == 0 else 48
for offset in range(start_offset, 280, 32):
design.add_nick(helix, offset, forward=helix % 2 == 1)
def export_idt_plate_file(design: sc.Design):
for strand in design.strands:
if strand != design.scaffold:
strand.set_default_idt(use_default_idt=True)
design.write_idt_plate_excel_file(use_default_plates=True)
def add_twist_correction_deletions(design: sc.Design) -> None:
for helix in range(24):
for offset in range(19, 286, 48):
design.add_deletion(helix, offset)
def add_staple_nicks(design: sc.Design) -> None:
for helix in range(24):
start_offset = 24 if helix % 2 == 0 else 40
for offset in range(start_offset, 272, 32):
design.add_nick(helix, offset, forward=helix % 2 == 1)
def add_twist_correct_deletions(design: sc.Design) -> None:
# I choose between 3 and 4 offset arbitrarily for twist-correction deletions for some reason,
# so they have to be hard-coded.
for col, offset in zip(range(4, 29, 3), [4, 3, 3, 4, 3, 3, 3, 3, 3]):
for helix in range(2, 18):
design.add_deletion(helix, 16 * col + offset)
def adjust_helix_grid_and_positions(design: sc.Design):
design.grid = sc.Grid.none
for helix in design.helices.values():
helix.grid_position = None
position3d = idx_to_position(helix.idx)
helix.position = position3d
def add_precursor_staples(design: sc.Design):
staples = [sc.Strand([sc.Domain(helix=helix, forward=helix % 2 == 1, start=8, end=296)])
for helix in range(24)]
for staple in staples:
design.add_strand(staple)
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)