def autoScafRaster(self, strands):
"""docstring for autoScafRaster"""
part = self.part()
idx = part.activeBaseIndex()
for i in range(1, len(strands)):
row1, col1, ss_idx1 = strands[i - 1] # previous strand
row2, col2, ss_idx2 = strands[i] # current strand
vh1 = part.virtualHelixAtCoord((row1, col1))
vh2 = part.virtualHelixAtCoord((row2, col2))
strand1 = vh1.scaffoldStrandSet()._strand_list[ss_idx1]
strand2 = vh2.scaffoldStrandSet()._strand_list[ss_idx2]
# determine if the pair of strands are neighbors
neighbors = part.getVirtualHelixNeighbors(vh1)
if vh2 in neighbors:
p2 = neighbors.index(vh2)
if vh2.number() % 2 == 1:
# resize and install external xovers
try:
# resize to the nearest prexover on either side of idx
new_lo1 = new_lo2 = util.nearest(idx,
part.getPreXoversHigh(StrandType.SCAFFOLD,
p2, max_idx=idx - 8))
new_hi = util.nearest(idx,
part.getPreXoversLow(StrandType.SCAFFOLD,
p2, min_idx=idx + 8))
if vh1.number() != 0: # after the first helix
new_lo1 = strand1.lowIdx() # leave alone the lowIdx
if vh2.number() != len(strands)-1: # before the last
new_lo2 = strand2.lowIdx() # leave alone the lowIdx
if strand1.canResizeTo(new_lo1, new_hi) and \
strand2.canResizeTo(new_lo2, new_hi):
strand1.resize((new_lo1, new_hi))
strand2.resize((new_lo2, new_hi))
else:
raise ValueError
# install xovers
part.createXover(strand1, new_hi, strand2, new_hi)
except ValueError:
pass # nearest not found in the expanded list
else:
# resize and install external xovers
idx = part.activeBaseIndex()
try:
# resize to the nearest prexover on either side of idx
new_lo = util.nearest(idx,
part.getPreXoversHigh(StrandType.SCAFFOLD,
p2, max_idx=idx - 8))
if strand1.canResizeTo(new_lo, strand1.highIdx()) and \
strand2.canResizeTo(new_lo, strand2.highIdx()):
strand1.resize((new_lo, strand1.highIdx()))
strand2.resize((new_lo, strand2.highIdx()))
# install xovers
part.createXover(strand1, new_lo, strand2, new_lo)
else:
raise ValueError
except ValueError:
pass # nearest not found in the expanded list
def autoScafRaster(self, strands):
"""docstring for autoScafRaster"""
part = self.part()
idx = part.activeBaseIndex()
for i in range(1, len(strands)):
row1, col1, ss_idx1 = strands[i - 1] # previous strand
row2, col2, ss_idx2 = strands[i] # current strand
vh1 = part.virtualHelixAtCoord((row1, col1))
vh2 = part.virtualHelixAtCoord((row2, col2))
strand1 = vh1.scaffoldStrandSet()._strand_list[ss_idx1]
strand2 = vh2.scaffoldStrandSet()._strand_list[ss_idx2]
# determine if the pair of strands are neighbors
neighbors = part.getVirtualHelixNeighbors(vh1)
if vh2 in neighbors:
p2 = neighbors.index(vh2)
if vh2.number() % 2 == 1:
# resize and install external xovers
try:
# resize to the nearest prexover on either side of idx
new_lo1 = new_lo2 = util.nearest(
idx,
part.getPreXoversHigh(StrandType.SCAFFOLD,
p2,
max_idx=idx - 8))
new_hi = util.nearest(
idx,
part.getPreXoversLow(StrandType.SCAFFOLD,
p2,
min_idx=idx + 8))
if vh1.number() != 0: # after the first helix
new_lo1 = strand1.lowIdx(
) # leave alone the lowIdx
if vh2.number() != len(strands) - 1: # before the last
new_lo2 = strand2.lowIdx(
) # leave alone the lowIdx
if strand1.canResizeTo(new_lo1, new_hi) and \
strand2.canResizeTo(new_lo2, new_hi):
strand1.resize((new_lo1, new_hi))
strand2.resize((new_lo2, new_hi))
else:
raise ValueError
# install xovers
part.createXover(strand1, new_hi, strand2, new_hi)
except ValueError:
pass # nearest not found in the expanded list
else:
# resize and install external xovers
idx = part.activeBaseIndex()
try:
# resize to the nearest prexover on either side of idx
new_lo = util.nearest(
idx,
part.getPreXoversHigh(StrandType.SCAFFOLD,
p2,
max_idx=idx - 8))
if strand1.canResizeTo(new_lo, strand1.highIdx()) and \
strand2.canResizeTo(new_lo, strand2.highIdx()):
strand1.resize((new_lo, strand1.highIdx()))
strand2.resize((new_lo, strand2.highIdx()))
# install xovers
part.createXover(strand1, new_lo, strand2, new_lo)
else:
raise ValueError
except ValueError:
pass # nearest not found in the expanded list
def autoScafMidSeam(self, strands):
"""docstring for autoScafMidSeam"""
part = self.part()
strand_type = StrandType.SCAFFOLD
idx = part.activeBaseIndex()
for i in range(1, len(strands)):
row1, col1, ss_idx1 = strands[i - 1] # previous strand
row2, col2, ss_idx2 = strands[i] # current strand
vh1 = part.virtualHelixAtCoord((row1, col1))
vh2 = part.virtualHelixAtCoord((row2, col2))
strand1 = vh1.scaffoldStrandSet()._strand_list[ss_idx1]
strand2 = vh2.scaffoldStrandSet()._strand_list[ss_idx2]
# determine if the pair of strands are neighbors
neighbors = part.getVirtualHelixNeighbors(vh1)
if vh2 in neighbors:
p2 = neighbors.index(vh2)
if vh2.number() % 2 == 1:
# resize and install external xovers
try:
# resize to the nearest prexover on either side of idx
new_lo = util.nearest(idx,
part.getPreXoversHigh(strand_type, p2, max_idx=idx - 10))
new_hi = util.nearest(idx,
part.getPreXoversLow(strand_type, p2, min_idx=idx + 10))
if strand1.canResizeTo(new_lo, new_hi) and \
strand2.canResizeTo(new_lo, new_hi):
# do the resize
strand1.resize((new_lo, new_hi))
strand2.resize((new_lo, new_hi))
# install xovers
part.createXover(strand1, new_hi, strand2, new_hi)
part.createXover(strand2, new_lo, strand1, new_lo)
except ValueError:
pass # nearest not found in the expanded list
# go back an install the internal xovers
if i > 2:
row0, col0, ss_idx0 = strands[i - 2] # two strands back
vh0 = part.virtualHelixAtCoord((row0, col0))
strand0 = vh0.scaffoldStrandSet()._strand_list[ss_idx0]
if vh0 in neighbors:
p0 = neighbors.index(vh0)
l0, h0 = strand0.idxs()
l1, h1 = strand1.idxs()
o_low, o_high = util.overlap(l0, h0, l1, h1)
try:
l_list = list(filter(lambda x: x > o_low and \
x < o_high,
part.getPreXoversLow(strand_type, p0)))
l_x = l_list[len(l_list) // 2]
h_list = list(filter(lambda x: x > o_low and \
x < o_high,
part.getPreXoversHigh(strand_type, p0)))
h_x = h_list[len(h_list) // 2]
# install high xover first
part.createXover(strand0, h_x, strand1, h_x)
# install low xover after getting new strands
# following the breaks caused by the high xover
strand3 = vh0.scaffoldStrandSet()._strand_list[ss_idx0]
strand4 = vh1.scaffoldStrandSet()._strand_list[ss_idx1]
part.createXover(strand4, l_x, strand3, l_x)
except IndexError:
pass # filter was unhappy
def autoScafMidSeam(self, strands):
"""docstring for autoScafMidSeam"""
part = self.part()
strand_type = StrandType.SCAFFOLD
idx = part.activeBaseIndex()
for i in range(1, len(strands)):
row1, col1, ss_idx1 = strands[i - 1] # previous strand
row2, col2, ss_idx2 = strands[i] # current strand
vh1 = part.virtualHelixAtCoord((row1, col1))
vh2 = part.virtualHelixAtCoord((row2, col2))
strand1 = vh1.scaffoldStrandSet()._strand_list[ss_idx1]
strand2 = vh2.scaffoldStrandSet()._strand_list[ss_idx2]
# determine if the pair of strands are neighbors
neighbors = part.getVirtualHelixNeighbors(vh1)
if vh2 in neighbors:
p2 = neighbors.index(vh2)
if vh2.number() % 2 == 1:
# resize and install external xovers
try:
# resize to the nearest prexover on either side of idx
new_lo = util.nearest(
idx,
part.getPreXoversHigh(strand_type,
p2,
max_idx=idx - 10))
new_hi = util.nearest(
idx,
part.getPreXoversLow(strand_type,
p2,
min_idx=idx + 10))
if strand1.canResizeTo(new_lo, new_hi) and \
strand2.canResizeTo(new_lo, new_hi):
# do the resize
strand1.resize((new_lo, new_hi))
strand2.resize((new_lo, new_hi))
# install xovers
part.createXover(strand1, new_hi, strand2, new_hi)
part.createXover(strand2, new_lo, strand1, new_lo)
except ValueError:
pass # nearest not found in the expanded list
# go back an install the internal xovers
if i > 2:
row0, col0, ss_idx0 = strands[i -
2] # two strands back
vh0 = part.virtualHelixAtCoord((row0, col0))
strand0 = vh0.scaffoldStrandSet()._strand_list[ss_idx0]
if vh0 in neighbors:
p0 = neighbors.index(vh0)
l0, h0 = strand0.idxs()
l1, h1 = strand1.idxs()
o_low, o_high = util.overlap(l0, h0, l1, h1)
try:
l_list = list(filter(lambda x: x > o_low and \
x < o_high,
part.getPreXoversLow(strand_type, p0)))
l_x = l_list[len(l_list) // 2]
h_list = list(filter(lambda x: x > o_low and \
x < o_high,
part.getPreXoversHigh(strand_type, p0)))
h_x = h_list[len(h_list) // 2]
# install high xover first
part.createXover(strand0, h_x, strand1, h_x)
# install low xover after getting new strands
# following the breaks caused by the high xover
strand3 = vh0.scaffoldStrandSet(
)._strand_list[ss_idx0]
strand4 = vh1.scaffoldStrandSet(
)._strand_list[ss_idx1]
part.createXover(strand4, l_x, strand3, l_x)
except IndexError:
pass # filter was unhappy