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 setComplementSequence(self, sequence_string, strand):
"""
This version takes anothers strand and only sets the indices that
align with the given complimentary strand
return the used portion of the sequence_string
As it depends which direction this is going, and strings are stored in
memory left to right, we need to test for is_drawn_5_to_3 to map the
reverse compliment appropriately, as we traverse overlapping strands.
We reverse the sequence ahead of time if we are applying it 5' to 3',
otherwise we reverse the sequence post parsing if it's 3' to 5'
Again, sequences are stored as strings in memory 5' to 3' so we need
to jump through these hoops to iterate 5' to 3' through them correctly
Perhaps it's wiser to merely store them left to right and reverse them
at draw time, or export time
"""
s_low_idx, s_high_idx = self._base_idx_low, self._base_idx_high
c_low_idx, c_high_idx = strand.idxs()
# get the ovelap
low_idx, high_idx = util.overlap(s_low_idx, s_high_idx, c_low_idx, c_high_idx)
# only get the characters we're using, while we're at it, make it the
# reverse compliment
total_length = self.totalLength()
# see if we are applying
if sequence_string == None:
# clear out string for in case of not total overlap
use_seq = ''.join([' ' for x in range(total_length)])
else: # use the string as is
use_seq = sequence_string[::-1] if self._is_drawn_5_to_3 \
else sequence_string
temp = array(array_type, sixb(use_seq))
if self._sequence == None:
temp_self = array(array_type, sixb(''.join([' ' for x in range(total_length)])))
else:
temp_self = array(array_type, sixb(self._sequence) if self._is_drawn_5_to_3 \
else sixb(self._sequence[::-1]))
# generate the index into the compliment string
a = self.insertionLengthBetweenIdxs(s_low_idx, low_idx - 1)
b = self.insertionLengthBetweenIdxs(low_idx, high_idx)
c = strand.insertionLengthBetweenIdxs(c_low_idx, low_idx - 1)
start = low_idx - c_low_idx + c
end = start + b + high_idx - low_idx + 1
temp_self[low_idx - s_low_idx + a:high_idx - s_low_idx + 1 + a + b] = \
temp[start:end]
# print "old sequence", self._sequence
self._sequence = tostring(temp_self)
# if we need to reverse it do it now
if not self._is_drawn_5_to_3:
self._sequence = self._sequence[::-1]
# test to see if the string is empty(), annoyingly expensive
if len(self._sequence.strip()) == 0:
self._sequence = None
# print "new sequence", self._sequence
return self._sequence
def setComplementSequence(self, sequence_string, strand):
"""This version takes anothers strand and only sets the indices that
align with the given complimentary strand.
As it depends which direction this is going, and strings are stored in
memory left to right, we need to test for is_forward to map the
reverse compliment appropriately, as we traverse overlapping strands.
We reverse the sequence ahead of time if we are applying it 5' to 3',
otherwise we reverse the sequence post parsing if it's 3' to 5'
Again, sequences are stored as strings in memory 5' to 3' so we need
to jump through these hoops to iterate 5' to 3' through them correctly
Perhaps it's wiser to merely store them left to right and reverse them
at draw time, or export time
Args:
sequence_string (str):
strand (Strand):
Returns:
str: the used portion of the sequence_string
"""
s_low_idx, s_high_idx = self._base_idx_low, self._base_idx_high
c_low_idx, c_high_idx = strand.idxs()
is_forward = self._is_forward
self_seq = self._sequence
# get the ovelap
low_idx, high_idx = util.overlap(s_low_idx, s_high_idx, c_low_idx,
c_high_idx)
# only get the characters we're using, while we're at it, make it the
# reverse compliment
total_length = self.totalLength()
# see if we are applying
if sequence_string is None:
# clear out string for in case of not total overlap
use_seq = ''.join([' ' for x in range(total_length)])
else: # use the string as is
use_seq = sequence_string[::-1] if is_forward else sequence_string
temp = array(ARRAY_TYPE, sixb(use_seq))
if self_seq is None:
temp_self = array(
ARRAY_TYPE, sixb(''.join([' ' for x in range(total_length)])))
else:
temp_self = array(
ARRAY_TYPE,
sixb(self_seq) if is_forward else sixb(self_seq[::-1]))
# generate the index into the compliment string
a = self.insertionLengthBetweenIdxs(s_low_idx, low_idx - 1)
b = self.insertionLengthBetweenIdxs(low_idx, high_idx)
c = strand.insertionLengthBetweenIdxs(c_low_idx, low_idx - 1)
start = low_idx - c_low_idx + c
end = start + b + high_idx - low_idx + 1
temp_self[low_idx - s_low_idx + a:high_idx - s_low_idx + 1 + a +
b] = temp[start:end]
# print("old sequence", self_seq)
self._sequence = tostring(temp_self)
# if we need to reverse it do it now
if not is_forward:
self._sequence = self._sequence[::-1]
# test to see if the string is empty(), annoyingly expensive
# if len(self._sequence.strip()) == 0:
if not self._sequence:
self._sequence = None
# print("new sequence", self._sequence)
return self._sequence
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
