def add_sequence(self, label, seq, align_to=None):
"""Append another sequence, aligned to the sequence 'contig' if it exists.
If there is no 'contig', then it starts at 0."""
if align_to is None or align_to not in self:
self[label] = aflist(0, seq, '-')
return self
template = ''.join(self[align_to].values)
((contig_offset, aligned_contig),
(seq_offset, aligned_seq)) = align.ssearch36(template, seq)
aligned1 = aflist(self[align_to].offset, aligned_contig, gap='-')
aligned2 = aflist(self[align_to].offset + seq_offset - contig_offset,
aligned_seq, '-')
assem, al1, al2 = conform_gaps(self, align_to, aligned1, aligned2)
assem[label] = al2
return assem
def add_sequence(self, label, seq, align_to=None):
"""Append another sequence, aligned to the sequence 'contig' if it exists.
If there is no 'contig', then it starts at 0."""
if align_to is None or align_to not in self:
self[label] = aflist(0, seq, '-')
return self
template = ''.join(self[align_to].values)
((contig_offset, aligned_contig),
(seq_offset, aligned_seq)) = align.ssearch36(template, seq)
aligned1 = aflist(self[align_to].offset, aligned_contig, gap='-')
aligned2 = aflist(self[align_to].offset + seq_offset - contig_offset,
aligned_seq, '-')
assem, al1, al2 = conform_gaps(self, align_to, aligned1, aligned2)
assem[label] = al2
return assem
def assemble(seq1, conf1, traces1, seq2, conf2, traces2):
"""Combine two reads into a contig.
Returns an Assembly with the reads (with used sections marked),
and a string specifying fate: 'both', 'strand 1', 'strand 2',
'none'. If the fate is not 'none', then there will be a key
'contig' in the Assembly.
"""
assert len(seq1) == len(conf1)
assert len(seq2) == len(conf2)
# Pull out high quality segments
hqint1, hqint2 = highqualityinterval(conf1), highqualityinterval(conf2)
segment1 = seq1[hqint1.left() : hqint1.right()] if hqint1.isproper() else ""
segment2 = seq2[hqint2.left() : hqint2.right()] if hqint2.isproper() else ""
# Align them
# If you were going to add assembly against a template, the major
# change would be to write a function that took segment1,
# segment2, and template, and returned a third argument
# (templateoffset, rawaltemplate), then called added the template
# in the Assembly lines below. The easiest path would probably be
# to make the template argument to assemble optional, defaulting
# to None, and call ssearch36 if it is None.
# The function to do the templated alignment would align both
# segments against the template, and then go through the two
# alignments to combine them (inserting -'s appropriately, etc.).
# For a very similar algorithm that may help in writing that, see assembly.conform_gaps.
(offset1, rawalsegment1), (offset2, rawalsegment2) = align.ssearch36(segment1, segment2)
alsegment1, alsegment2 = (
aflist(offset1, rawalsegment1, gap="-", trackclass="nucleotide"),
aflist(offset2, rawalsegment2, gap="-", trackclass="nucleotide"),
)
alhqint1 = ProperInterval(offset1, offset1 + alsegment1.width())
alhqint2 = ProperInterval(offset2, offset2 + alsegment2.width())
alseq1, alseq2 = extend(alsegment1, hqint1, aflist(0, seq1, "-")), extend(alsegment2, hqint2, aflist(0, seq2, "-"))
alconf1, alconf2 = tracealong(conf1, alseq1), tracealong(conf2, alseq2)
altraces1, altraces2 = (
tracealong(traces1, alseq1) if traces1 else None,
tracealong(traces2, alseq2) if traces2 else None,
)
for i, s in (
(alhqint1, alseq1),
(alhqint1, alconf1),
(alhqint1, altraces1),
(alhqint2, alseq2),
(alhqint2, alconf2),
(alhqint2, altraces2),
):
if s is None:
continue
if i.isempty():
s.appendfeature(interval(neginf, posinf, name="unused", red=0, green=0, blue=0, alpha=0.5))
else:
if i.left() > s.left():
s.appendfeature(interval(neginf, i.left(), name="leftunused", red=0, green=0, blue=0, alpha=0.5))
if i.right() < s.right():
s.appendfeature(interval(i.right(), posinf, name="rightunused", red=0, green=0, blue=0, alpha=0.5))
assert alsegment1.width() == alconf1[alhqint1].width()
assert altraces1 is None or alsegment1.width() == altraces1[alhqint1].width()
assert alsegment2.width() == alconf2[alhqint2].width()
assert altraces2 is None or alsegment2.width() == altraces2[alhqint2].width()
contig = combine((alsegment1, alconf1[alhqint1]), (alsegment2, alconf2[alhqint2]))
alconf1.setmeta("trackclass", "integer")
alconf2.setmeta("trackclass", "integer")
if altraces1:
altraces1.setmeta("trackclass", "svg")
if altraces2:
altraces2.setmeta("trackclass", "svg")
alseq1.setmeta("trackclass", "nucleotide")
alseq2.setmeta("trackclass", "nucleotide")
contig.setmeta("trackclass", "nucleotide")
if alsegment1.width() != 0 and alsegment2.width() != 0: # both strands
a = Assembly()
if altraces1:
a["traces 1"] = altraces1
a["confidences 1"] = alconf1
a["bases 1"] = alseq1
if altraces2:
a["traces 2"] = altraces2
a["confidences 2"] = alconf2
a["bases 2"] = alseq2
a["contig"] = contig
return a.toorigin()
elif alsegment1.width() != 0: # strand 1 only
a = Assembly()
if altraces2:
a["traces 2"] = (
ProperList(
0,
traces2,
gap=None,
trackclass="svg",
features=[interval(neginf, posinf, name="unused", red=0, green=0, blue=0, alpha=0.5)],
)
>> alconf1.left()
)
a["confidences 2"] = (
ProperList(
0,
conf2,
gap=None,
trackclass="integer",
features=[interval(neginf, posinf, name="unused", red=0, green=0, blue=0, alpha=0.5)],
)
>> alconf1.left()
)
a["bases 2"] = (
ProperList(
0,
seq2,
gap="-",
trackclass="nucleotide",
features=[interval(neginf, posinf, name="unused", red=0, green=0, blue=0, alpha=0.5)],
)
>> alconf1.left()
)
if altraces1:
a["traces 1"] = altraces1
a["confidences 1"] = alconf1
a["bases 1"] = alseq1
a["contig"] = contig
return a.toorigin()
elif alsegment2.width() != 0: # strand 2 only
a = Assembly()
if altraces1:
a["traces 1"] = (
ProperList(
0,
traces1,
gap=None,
trackclass="svg",
features=[interval(neginf, posinf, name="unused", red=0, green=0, blue=0, alpha=0.5)],
)
>> alconf2.left()
)
a["confidences 1"] = (
ProperList(
0,
conf1,
gap=None,
trackclass="integer",
features=[interval(neginf, posinf, name="unused", red=0, green=0, blue=0, alpha=0.5)],
)
>> alconf2.left()
)
a["bases 1"] = (
ProperList(
0,
seq1,
gap="-",
trackclass="nucleotide",
features=[interval(neginf, posinf, name="unused", red=0, green=0, blue=0, alpha=0.5)],
)
>> alconf2.left()
)
if altraces2:
a["traces 2"] = altraces2
a["confidences 2"] = alconf2
a["bases 2"] = alseq2
a["contig"] = contig
return a.toorigin()
else:
a = Assembly()
if traces1:
a["traces 1"] = ProperList(
0,
traces1,
gap=None,
trackclass="svg",
features=[interval(neginf, posinf, name="unused", red=0, green=0, blue=0, alpha=0.5)],
)
a["confidences 1"] = ProperList(
0,
conf1,
gap=None,
trackclass="integer",
features=[interval(neginf, posinf, name="unused", red=0, green=0, blue=0, alpha=0.5)],
)
a["bases 1"] = ProperList(
0,
seq1,
gap="-",
trackclass="nucleotide",
features=[interval(neginf, posinf, name="unused", red=0, green=0, blue=0, alpha=0.5)],
)
if traces2:
a["traces 2"] = ProperList(
0,
traces2,
gap=None,
trackclass="svg",
features=[interval(neginf, posinf, name="unused", red=0, green=0, blue=0, alpha=0.5)],
)
a["confidences 2"] = ProperList(
0,
conf2,
gap=None,
trackclass="integer",
features=[interval(neginf, posinf, name="unused", red=0, green=0, blue=0, alpha=0.5)],
)
a["bases 2"] = ProperList(
0,
seq2,
gap="-",
trackclass="nucleotide",
features=[interval(neginf, posinf, name="unused", red=0, green=0, blue=0, alpha=0.5)],
)
return a
def assemble(seq1, conf1, traces1, seq2, conf2, traces2):
"""Combine two reads into a contig.
Returns an Assembly with the reads (with used sections marked),
and a string specifying fate: 'both', 'strand 1', 'strand 2',
'none'. If the fate is not 'none', then there will be a key
'contig' in the Assembly.
"""
assert len(seq1) == len(conf1)
assert len(seq2) == len(conf2)
# Pull out high quality segments
hqint1, hqint2 = highqualityinterval(conf1), highqualityinterval(conf2)
segment1 = seq1[hqint1.left():hqint1.right()] if hqint1.isproper() else ""
segment2 = seq2[hqint2.left():hqint2.right()] if hqint2.isproper() else ""
# Align them
# If you were going to add assembly against a template, the major
# change would be to write a function that took segment1,
# segment2, and template, and returned a third argument
# (templateoffset, rawaltemplate), then called added the template
# in the Assembly lines below. The easiest path would probably be
# to make the template argument to assemble optional, defaulting
# to None, and call ssearch36 if it is None.
# The function to do the templated alignment would align both
# segments against the template, and then go through the two
# alignments to combine them (inserting -'s appropriately, etc.).
# For a very similar algorithm that may help in writing that, see assembly.conform_gaps.
(offset1,
rawalsegment1), (offset2,
rawalsegment2) = align.ssearch36(segment1, segment2)
alsegment1, alsegment2 = aflist(offset1, rawalsegment1, gap='-', trackclass='nucleotide'), \
aflist(offset2, rawalsegment2, gap='-', trackclass='nucleotide')
alhqint1 = ProperInterval(offset1, offset1 + alsegment1.width())
alhqint2 = ProperInterval(offset2, offset2 + alsegment2.width())
alseq1, alseq2 = extend(alsegment1, hqint1, aflist(0,seq1,'-')), \
extend(alsegment2, hqint2, aflist(0,seq2,'-'))
alconf1, alconf2 = tracealong(conf1, alseq1), tracealong(conf2, alseq2)
altraces1, altraces2 = tracealong(traces1, alseq1) if traces1 else None, \
tracealong(traces2, alseq2) if traces2 else None
for i,s in (alhqint1, alseq1), (alhqint1, alconf1), (alhqint1, altraces1), \
(alhqint2, alseq2), (alhqint2, alconf2), (alhqint2, altraces2):
if s is None:
continue
if i.isempty():
s.appendfeature(
interval(neginf,
posinf,
name='unused',
red=0,
green=0,
blue=0,
alpha=0.5))
else:
if i.left() > s.left():
s.appendfeature(
interval(neginf,
i.left(),
name='leftunused',
red=0,
green=0,
blue=0,
alpha=0.5))
if i.right() < s.right():
s.appendfeature(
interval(i.right(),
posinf,
name='rightunused',
red=0,
green=0,
blue=0,
alpha=0.5))
assert alsegment1.width() == alconf1[alhqint1].width()
assert altraces1 is None or alsegment1.width(
) == altraces1[alhqint1].width()
assert alsegment2.width() == alconf2[alhqint2].width()
assert altraces2 is None or alsegment2.width(
) == altraces2[alhqint2].width()
contig = combine((alsegment1, alconf1[alhqint1]),
(alsegment2, alconf2[alhqint2]))
alconf1.setmeta('trackclass', 'integer')
alconf2.setmeta('trackclass', 'integer')
if altraces1:
altraces1.setmeta('trackclass', 'svg')
if altraces2:
altraces2.setmeta('trackclass', 'svg')
alseq1.setmeta('trackclass', 'nucleotide')
alseq2.setmeta('trackclass', 'nucleotide')
contig.setmeta('trackclass', 'nucleotide')
if alsegment1.width() != 0 and alsegment2.width() != 0: # both strands
a = Assembly()
if altraces1:
a['traces 1'] = altraces1
a['confidences 1'] = alconf1
a['bases 1'] = alseq1
if altraces2:
a['traces 2'] = altraces2
a['confidences 2'] = alconf2
a['bases 2'] = alseq2
a['contig'] = contig
return a.toorigin()
elif alsegment1.width() != 0: # strand 1 only
a = Assembly()
if altraces2:
a['traces 2'] = ProperList(0,
traces2,
gap=None,
trackclass='svg',
features=[
interval(neginf,
posinf,
name='unused',
red=0,
green=0,
blue=0,
alpha=0.5)
]) >> alconf1.left()
a['confidences 2'] = ProperList(0,
conf2,
gap=None,
trackclass='integer',
features=[
interval(neginf,
posinf,
name='unused',
red=0,
green=0,
blue=0,
alpha=0.5)
]) >> alconf1.left()
a['bases 2'] = ProperList(0,
seq2,
gap='-',
trackclass='nucleotide',
features=[
interval(neginf,
posinf,
name='unused',
red=0,
green=0,
blue=0,
alpha=0.5)
]) >> alconf1.left()
if altraces1:
a['traces 1'] = altraces1
a['confidences 1'] = alconf1
a['bases 1'] = alseq1
a['contig'] = contig
return a.toorigin()
elif alsegment2.width() != 0: # strand 2 only
a = Assembly()
if altraces1:
a['traces 1'] = ProperList(0,
traces1,
gap=None,
trackclass='svg',
features=[
interval(neginf,
posinf,
name='unused',
red=0,
green=0,
blue=0,
alpha=0.5)
]) >> alconf2.left()
a['confidences 1'] = ProperList(0,
conf1,
gap=None,
trackclass='integer',
features=[
interval(neginf,
posinf,
name='unused',
red=0,
green=0,
blue=0,
alpha=0.5)
]) >> alconf2.left()
a['bases 1'] = ProperList(0,
seq1,
gap='-',
trackclass='nucleotide',
features=[
interval(neginf,
posinf,
name='unused',
red=0,
green=0,
blue=0,
alpha=0.5)
]) >> alconf2.left()
if altraces2:
a['traces 2'] = altraces2
a['confidences 2'] = alconf2
a['bases 2'] = alseq2
a['contig'] = contig
return a.toorigin()
else:
a = Assembly()
if traces1:
a['traces 1'] = ProperList(0,
traces1,
gap=None,
trackclass='svg',
features=[
interval(neginf,
posinf,
name='unused',
red=0,
green=0,
blue=0,
alpha=0.5)
])
a['confidences 1'] = ProperList(0,
conf1,
gap=None,
trackclass='integer',
features=[
interval(neginf,
posinf,
name='unused',
red=0,
green=0,
blue=0,
alpha=0.5)
])
a['bases 1'] = ProperList(0,
seq1,
gap='-',
trackclass='nucleotide',
features=[
interval(neginf,
posinf,
name='unused',
red=0,
green=0,
blue=0,
alpha=0.5)
])
if traces2:
a['traces 2'] = ProperList(0,
traces2,
gap=None,
trackclass='svg',
features=[
interval(neginf,
posinf,
name='unused',
red=0,
green=0,
blue=0,
alpha=0.5)
])
a['confidences 2'] = ProperList(0,
conf2,
gap=None,
trackclass='integer',
features=[
interval(neginf,
posinf,
name='unused',
red=0,
green=0,
blue=0,
alpha=0.5)
])
a['bases 2'] = ProperList(0,
seq2,
gap='-',
trackclass='nucleotide',
features=[
interval(neginf,
posinf,
name='unused',
red=0,
green=0,
blue=0,
alpha=0.5)
])
return a
