def decode(document: DocT, obj: dict, emit_signals: bool = True):
"""Parses a dictionary (obj) created from reading a json file and uses it
to populate the given document with model data.
Args:
document:
obj:
emit_signals: whether to signal views
Raises:
IOError, AssertionError, TypeError
"""
num_bases = len(obj['vstrands'][0]['scaf'])
if num_bases % 32 == 0:
lattice_type = LatticeEnum.SQUARE
grid_type = GridEnum.SQUARE
elif num_bases % 21 == 0:
lattice_type = LatticeEnum.HONEYCOMB
grid_type = GridEnum.HONEYCOMB
else:
raise IOError("error decoding number of bases")
part = None
# DETERMINE MAX ROW,COL
max_row_json = max_col_json = 0
for helix in obj['vstrands']:
max_row_json = max(max_row_json, int(helix['row'])+1)
max_col_json = max(max_col_json, int(helix['col'])+1)
# CREATE PART ACCORDING TO LATTICE TYPE
if lattice_type == LatticeEnum.HONEYCOMB:
doLattice = HoneycombDnaPart.legacyLatticeCoordToPositionXY
isEven = HoneycombDnaPart.isEvenParity
elif lattice_type == LatticeEnum.SQUARE:
doLattice = SquareDnaPart.legacyLatticeCoordToPositionXY
isEven = SquareDnaPart.isEvenParity
else:
raise TypeError("Lattice type not recognized")
part = document.createNucleicAcidPart(grid_type=grid_type, use_undostack=False)
part.setActive(True)
document.setGridType(grid_type)
document.setSliceOrGridViewVisible(OrthoViewEnum.SLICE)
setBatch(True)
# POPULATE VIRTUAL HELICES
ordered_id_list = []
vh_num_to_coord = {}
min_row, max_row = 10000, -10000
min_col, max_col = 10000, -10000
# find row, column limits
for helix in obj['vstrands']:
row = helix['row']
if row < min_row:
min_row = row
if row > max_row:
max_row = row
col = helix['col']
if col < min_col:
min_col = col
if col > max_col:
max_col = col
# end for
delta_row = (max_row + min_row) // 2
# # 2 LINES COMMENTED OUT BY NC, doesn't appear to be necessary for honeycomb
# if delta_row & 0:
if delta_row & 1:
delta_row += 1
delta_column = (max_col + min_col) // 2
# if delta_column & 0:
if delta_column & 1:
delta_column += 1
print("Found cadnano version 2 file")
# print("\trows(%d, %d): avg: %d" % (min_row, max_row, delta_row))
# print("\tcolumns(%d, %d): avg: %d" % (min_col, max_col, delta_column))
for helix in obj['vstrands']:
vh_num = helix['num']
row = helix['row']
col = helix['col']
scaf = helix['scaf']
# align row and columns to the center 0, 0
if HoneycombDnaPart.isEvenParity(row, col):
coord = (row - delta_row, col - delta_column)
else:
coord = (row - delta_row, col - delta_column)
vh_num_to_coord[vh_num] = coord
ordered_id_list.append(vh_num)
# end for
# make sure we retain the original order
radius = DEFAULT_RADIUS
for vh_num in sorted(vh_num_to_coord.keys()):
row, col = vh_num_to_coord[vh_num]
x, y = doLattice(radius, row, col)
part.createVirtualHelix(x, y, 0., num_bases,
id_num=vh_num, use_undostack=False)
# zoom to fit
if emit_signals:
part.partZDimensionsChangedSignal.emit(part, *part.zBoundsIds(), True)
if not getReopen():
setBatch(False)
part.setImportedVHelixOrder(ordered_id_list)
setReopen(False)
setBatch(False)
# INSTALL STRANDS AND COLLECT XOVER LOCATIONS
scaf_seg = defaultdict(list)
scaf_xo = defaultdict(list)
stap_seg = defaultdict(list)
stap_xo = defaultdict(list)
try:
for helix in obj['vstrands']:
vh_num = helix['num']
row, col = vh_num_to_coord[vh_num]
scaf = helix['scaf']
stap = helix['stap']
insertions = helix['loop']
skips = helix['skip']
if isEven(row, col):
scaf_strand_set, stap_strand_set = part.getStrandSets(vh_num)
else:
stap_strand_set, scaf_strand_set = part.getStrandSets(vh_num)
# validate file serialization of lists
assert(len(scaf) == len(stap) and
len(scaf) == len(insertions) and
len(insertions) == len(skips))
# read scaffold segments and xovers
for i in range(len(scaf)):
five_vh, five_idx, three_vh, three_idx = scaf[i]
if five_vh == -1 and three_vh == -1:
continue # null base
if isSegmentStartOrEnd(StrandEnum.SCAFFOLD, vh_num, i, five_vh,
five_idx, three_vh, three_idx):
scaf_seg[vh_num].append(i)
if five_vh != vh_num and three_vh != vh_num: # special case
scaf_seg[vh_num].append(i) # end segment on a double crossover
if is3primeXover(StrandEnum.SCAFFOLD, vh_num, i, three_vh, three_idx):
scaf_xo[vh_num].append((i, three_vh, three_idx))
assert (len(scaf_seg[vh_num]) % 2 == 0)
# install scaffold segments
for i in range(0, len(scaf_seg[vh_num]), 2):
low_idx = scaf_seg[vh_num][i]
high_idx = scaf_seg[vh_num][i + 1]
scaf_strand_set.createStrand(low_idx, high_idx, use_undostack=False)
# read staple segments and xovers
for i in range(len(stap)):
five_vh, five_idx, three_vh, three_idx = stap[i]
if five_vh == -1 and three_vh == -1:
continue # null base
if isSegmentStartOrEnd(StrandEnum.STAPLE, vh_num, i, five_vh,
five_idx, three_vh, three_idx):
stap_seg[vh_num].append(i)
if five_vh != vh_num and three_vh != vh_num: # special case
stap_seg[vh_num].append(i) # end segment on a double crossover
if is3primeXover(StrandEnum.STAPLE, vh_num, i, three_vh, three_idx):
stap_xo[vh_num].append((i, three_vh, three_idx))
assert (len(stap_seg[vh_num]) % 2 == 0)
# install staple segments
for i in range(0, len(stap_seg[vh_num]), 2):
low_idx = stap_seg[vh_num][i]
high_idx = stap_seg[vh_num][i + 1]
stap_strand_set.createStrand(low_idx, high_idx, use_undostack=False)
part.refreshSegments(vh_num)
# end for
except AssertionError:
print("Unrecognized file format.")
raise
# INSTALL XOVERS
for helix in obj['vstrands']:
vh_num = helix['num']
row, col = vh_num_to_coord[vh_num]
if isEven(row, col):
scaf_strand_set, stap_strand_set = part.getStrandSets(vh_num)
else:
stap_strand_set, scaf_strand_set = part.getStrandSets(vh_num)
# install scaffold xovers
for (idx5p, to_vh_num, idx3p) in scaf_xo[vh_num]:
# idx3p is 3' end of strand5p, idx5p is 5' end of strand3p
try:
strand5p = scaf_strand_set.getStrand(idx5p)
except Exception:
print(vh_num, idx5p)
print(scaf_strand_set.strand_heap)
print(stap_strand_set.strand_heap)
raise
coord = vh_num_to_coord[to_vh_num]
if isEven(*coord):
to_scaf_strand_set, to_stap_strand_set = part.getStrandSets(to_vh_num)
else:
to_stap_strand_set, to_scaf_strand_set = part.getStrandSets(to_vh_num)
strand3p = to_scaf_strand_set.getStrand(idx3p)
part.createXover(strand5p, idx5p,
strand3p, idx3p,
allow_reordering=True,
update_oligo=False,
use_undostack=False)
# install staple xovers
for (idx5p, to_vh_num, idx3p) in stap_xo[vh_num]:
# idx3p is 3' end of strand5p, idx5p is 5' end of strand3p
strand5p = stap_strand_set.getStrand(idx5p)
coord = vh_num_to_coord[to_vh_num]
if isEven(*coord):
to_scaf_strand_set, to_stap_strand_set = part.getStrandSets(to_vh_num)
else:
to_stap_strand_set, to_scaf_strand_set = part.getStrandSets(to_vh_num)
strand3p = to_stap_strand_set.getStrand(idx3p)
part.createXover(strand5p, idx5p,
strand3p, idx3p,
allow_reordering=True,
update_oligo=False,
use_undostack=False)
# need to heal all oligo connections into a continuous
# oligo for the next steps
RefreshOligosCommand(part).redo()
# COLORS, INSERTIONS, SKIPS
for helix in obj['vstrands']:
vh_num = helix['num']
row, col = vh_num_to_coord[vh_num]
scaf = helix['scaf']
stap = helix['stap']
insertions = helix['loop']
skips = helix['skip']
if isEven(row, col):
scaf_strand_set, stap_strand_set = part.getStrandSets(vh_num)
else:
stap_strand_set, scaf_strand_set = part.getStrandSets(vh_num)
# install insertions and skips
for base_idx in range(len(stap)):
sum_of_insert_skip = insertions[base_idx] + skips[base_idx]
if sum_of_insert_skip != 0:
strand = scaf_strand_set.getStrand(base_idx)
strand.addInsertion(base_idx,
sum_of_insert_skip,
use_undostack=False)
# end for
# populate colors
for base_idx, color_number in helix['stap_colors']:
color = intToColorHex(color_number)
strand = stap_strand_set.getStrand(base_idx)
strand.oligo().applyColor(color, use_undostack=False)
if 'oligos' in obj:
for oligo in obj['oligos']:
vh_num = oligo['vh_num']
idx = oligo['idx']
seq = str(oligo['seq']) if oligo['seq'] is not None else ''
if seq != '':
coord = vh_num_to_coord[vh_num]
if isEven(*coord):
scaf_ss, stap_ss = part.getStrandSets(vh_num)
else:
stap_ss, scaf_ss = part.getStrandSets(vh_num)
strand = scaf_ss.getStrand(idx)
# print "sequence", seq, vh, idx, strand.oligo()._strand5p
strand.oligo().applySequence(seq, use_undostack=False)
if 'modifications' in obj:
for mod_id, item in obj['modifications'].items():
if mod_id != 'int_instances' and mod_id != 'ext_instances':
part.createMod(item, mod_id)
for key, mid in obj['modifications']['ext_instances'].items():
# strand, idx, coord, isstaple = part.getModStrandIdx(key)
strand, idx = part.getModStrandIdx(key)
try:
strand.addMods(document, mid, idx, use_undostack=False)
except Exception:
print(strand, idx)
raise
for key, mid in obj['modifications']['int_instances'].items():
# strand, idx, coord, isstaple = part.getModStrandIdx(key)
strand, idx = part.getModStrandIdx(key)
try:
strand.addMods(document, mid, idx, use_undostack=False)
except Exception:
print(strand, idx)
raise
def decode(document, obj, emit_signals=False):
"""Parses a dictionary (obj) created from reading a json file and uses it
to populate the given document with model data.
"""
num_bases = len(obj['vstrands'][0]['scaf'])
if num_bases % 32 == 0:
lattice_type = LatticeType.SQUARE
elif num_bases % 21 == 0:
lattice_type = LatticeType.HONEYCOMB
else:
raise IOError("error decoding number of bases")
part = None
# DETERMINE MAX ROW,COL
max_row_json = max_col_json = 0
for helix in obj['vstrands']:
max_row_json = max(max_row_json, int(helix['row'])+1)
max_col_json = max(max_col_json, int(helix['col'])+1)
# CREATE PART ACCORDING TO LATTICE TYPE
if lattice_type == LatticeType.HONEYCOMB:
doLattice = HoneycombDnaPart.legacyLatticeCoordToPositionXY
isEven = HoneycombDnaPart.isEvenParity
elif lattice_type == LatticeType.SQUARE:
doLattice = SquareDnaPart.legacyLatticeCoordToPositionXY
isEven = SquareDnaPart.isEvenParity
else:
raise TypeError("Lattice type not recognized")
part = document.createNucleicAcidPart(use_undostack=False)
part.setActive(True)
setBatch(True)
delta = num_bases - 42
# POPULATE VIRTUAL HELICES
ordered_id_list = []
vh_num_to_coord = {}
min_row, max_row = 10000, -10000
min_col, max_col = 10000, -10000
# find row, column limits
for helix in obj['vstrands']:
row = helix['row']
if row < min_row:
min_row = row
if row > max_row:
max_row = row
col = helix['col']
if col < min_col:
min_col = col
if col > max_col:
max_col = col
# end for
delta_row = (max_row + min_row) // 2
# 2 LINES COMMENTED OUT BY NC, doesn't appear to be necessary for honeycomb
# if delta_row & 1:
# delta_row += 1
delta_column = (max_col + min_col) // 2
if delta_column & 1:
delta_column += 1
# print("Found cadnano version 2 file")
# print("\trows(%d, %d): avg: %d" % (min_row, max_row, delta_row))
# print("\tcolumns(%d, %d): avg: %d" % (min_col, max_col, delta_column))
for helix in obj['vstrands']:
vh_num = helix['num']
row = helix['row']
col = helix['col']
scaf= helix['scaf']
# align row and columns to the center 0, 0
coord = (row - delta_row, col - delta_column)
vh_num_to_coord[vh_num] = coord
ordered_id_list.append(vh_num)
# end for
# make sure we retain the original order
radius = DEFAULT_RADIUS
for vh_num in sorted(vh_num_to_coord.keys()):
row, col = vh_num_to_coord[vh_num]
x, y = doLattice(radius, row, col)
# print("%d:" % vh_num, x, y)
part.createVirtualHelix(x, y, 0., num_bases,
id_num=vh_num, use_undostack=False)
# zoom to fit
if emit_signals:
part.partZDimensionsChangedSignal.emit(part, *part.zBoundsIds(), True)
if not getReopen():
setBatch(False)
part.setImportedVHelixOrder(ordered_id_list)
setReopen(False)
setBatch(False)
# INSTALL STRANDS AND COLLECT XOVER LOCATIONS
scaf_seg = defaultdict(list)
scaf_xo = defaultdict(list)
stap_seg = defaultdict(list)
stap_xo = defaultdict(list)
try:
for helix in obj['vstrands']:
vh_num = helix['num']
row, col = vh_num_to_coord[vh_num]
scaf = helix['scaf']
stap = helix['stap']
insertions = helix['loop']
skips = helix['skip']
if isEven(row, col):
scaf_strand_set, stap_strand_set = part.getStrandSets(vh_num)
else:
stap_strand_set, scaf_strand_set = part.getStrandSets(vh_num)
# validate file serialization of lists
assert( len(scaf) == len(stap) and
len(scaf) == len(insertions) and
len(insertions) == len(skips) )
# read scaffold segments and xovers
for i in range(len(scaf)):
five_vh, five_idx, three_vh, three_idx = scaf[i]
if five_vh == -1 and three_vh == -1:
continue # null base
if isSegmentStartOrEnd(StrandType.SCAFFOLD, vh_num, i, five_vh,\
five_idx, three_vh, three_idx):
scaf_seg[vh_num].append(i)
if five_vh != vh_num and three_vh != vh_num: # special case
scaf_seg[vh_num].append(i) # end segment on a double crossover
if is3primeXover(StrandType.SCAFFOLD, vh_num, i, three_vh, three_idx):
scaf_xo[vh_num].append((i, three_vh, three_idx))
assert (len(scaf_seg[vh_num]) % 2 == 0)
# install scaffold segments
for i in range(0, len(scaf_seg[vh_num]), 2):
low_idx = scaf_seg[vh_num][i]
high_idx = scaf_seg[vh_num][i + 1]
scaf_strand_set.createStrand(low_idx, high_idx, use_undostack=False)
# read staple segments and xovers
for i in range(len(stap)):
five_vh, five_idx, three_vh, three_idx = stap[i]
if five_vh == -1 and three_vh == -1:
continue # null base
if isSegmentStartOrEnd(StrandType.STAPLE, vh_num, i, five_vh,\
five_idx, three_vh, three_idx):
stap_seg[vh_num].append(i)
if five_vh != vh_num and three_vh != vh_num: # special case
stap_seg[vh_num].append(i) # end segment on a double crossover
if is3primeXover(StrandType.STAPLE, vh_num, i, three_vh, three_idx):
stap_xo[vh_num].append((i, three_vh, three_idx))
assert (len(stap_seg[vh_num]) % 2 == 0)
# install staple segments
for i in range(0, len(stap_seg[vh_num]), 2):
low_idx = stap_seg[vh_num][i]
high_idx = stap_seg[vh_num][i + 1]
stap_strand_set.createStrand(low_idx, high_idx, use_undostack=False)
part.refreshSegments(vh_num)
# end for
except AssertionError:
print("Unrecognized file format.")
raise
# INSTALL XOVERS
for helix in obj['vstrands']:
vh_num = helix['num']
row, col = vh_num_to_coord[vh_num]
if isEven(row, col):
scaf_strand_set, stap_strand_set = part.getStrandSets(vh_num)
else:
stap_strand_set, scaf_strand_set = part.getStrandSets(vh_num)
# install scaffold xovers
for (idx5p, to_vh_num, idx3p) in scaf_xo[vh_num]:
# idx3p is 3' end of strand5p, idx5p is 5' end of strand3p
try:
strand5p = scaf_strand_set.getStrand(idx5p)
except:
print(vh_num, idx5p)
print(scaf_strand_set.strand_heap)
print(stap_strand_set.strand_heap)
raise
coord = vh_num_to_coord[to_vh_num]
if isEven(*coord):
to_scaf_strand_set, to_stap_strand_set = part.getStrandSets(to_vh_num)
else:
to_stap_strand_set, to_scaf_strand_set = part.getStrandSets(to_vh_num)
strand3p = to_scaf_strand_set.getStrand(idx3p)
part.createXover( strand5p, idx5p,
strand3p, idx3p,
allow_reordering=True,
update_oligo=False,
use_undostack=False)
# install staple xovers
for (idx5p, to_vh_num, idx3p) in stap_xo[vh_num]:
# idx3p is 3' end of strand5p, idx5p is 5' end of strand3p
strand5p = stap_strand_set.getStrand(idx5p)
coord = vh_num_to_coord[to_vh_num]
if isEven(*coord):
to_scaf_strand_set, to_stap_strand_set = part.getStrandSets(to_vh_num)
else:
to_stap_strand_set, to_scaf_strand_set = part.getStrandSets(to_vh_num)
strand3p = to_stap_strand_set.getStrand(idx3p)
part.createXover( strand5p, idx5p,
strand3p, idx3p,
allow_reordering=True,
update_oligo=False,
use_undostack=False)
# need to heal all oligo connections into a continuous
# oligo for the next steps
RefreshOligosCommand(part).redo()
# COLORS, INSERTIONS, SKIPS
for helix in obj['vstrands']:
vh_num = helix['num']
row, col = vh_num_to_coord[vh_num]
scaf = helix['scaf']
stap = helix['stap']
insertions = helix['loop']
skips = helix['skip']
if isEven(row, col):
scaf_strand_set, stap_strand_set = part.getStrandSets(vh_num)
else:
stap_strand_set, scaf_strand_set = part.getStrandSets(vh_num)
# install insertions and skips
for base_idx in range(len(stap)):
sum_of_insert_skip = insertions[base_idx] + skips[base_idx]
if sum_of_insert_skip != 0:
strand = scaf_strand_set.getStrand(base_idx)
strand.addInsertion(base_idx,
sum_of_insert_skip,
use_undostack=False)
# end for
# populate colors
for base_idx, color_number in helix['stap_colors']:
color = intToColorHex(color_number)
strand = stap_strand_set.getStrand(base_idx)
strand.oligo().applyColor(color, use_undostack=False)
if 'oligos' in obj:
for oligo in obj['oligos']:
vh_num = oligo['vh_num']
idx = oligo['idx']
seq = str(oligo['seq']) if oligo['seq'] is not None else ''
if seq != '':
coord = vh_num_to_coord[vh_num]
if isEven(*coord):
scaf_ss, stap_ss = part.getStrandSets(vh_num)
else:
stap_ss, scaf_ss = part.getStrandSets(vh_num)
strand = scaf_ss.getStrand(idx)
# print "sequence", seq, vh, idx, strand.oligo()._strand5p
strand.oligo().applySequence(seq, use_undostack=False)
if 'modifications' in obj:
for mod_id, item in obj['modifications'].items():
if mod_id != 'int_instances' and mod_id != 'ext_instances':
part.createMod(item, mod_id)
for key, mid in obj['modifications']['ext_instances'].items():
# strand, idx, coord, isstaple = part.getModStrandIdx(key)
strand, idx = part.getModStrandIdx(key)
try:
strand.addMods(document, mid, idx, use_undostack=False)
except:
print(strand, idx)
raise
for key, mid in obj['modifications']['int_instances'].items():
# strand, idx, coord, isstaple = part.getModStrandIdx(key)
strand, idx = part.getModStrandIdx(key)
try:
strand.addMods(document, mid, idx, use_undostack=False)
except:
print(strand, idx)
raise