def get_aligns(self,
species,
chrom,
start,
end,
mainspecies=lambda keys: keys[0],
collapse=False):
"""By default assumes main species is 1st sequence"""
# get records for this region
records = self.get(species, chrom, start, end)
records.sort(key=lambda x: x["start"])
# read alignments
alns = []
for record in records:
aln = fasta.read_fasta(record["filename"])
# collapse alignment
if collapse:
ind = util.findneq("-", aln[mainspecies(aln.keys())])
for key, seq in aln.iteritems():
if len(seq) != 0:
aln[key] = "".join(util.mget(seq, ind))
l2a = alignlib.local2align(aln[mainspecies(aln.keys())])
# trim front
if start > record["start"]:
trimstart = l2a[start - record["start"]]
else:
trimstart = 0
# trim end
if end < record["end"]:
trimend = l2a[-(record["end"] - end)]
else:
trimend = aln.alignlen()
# perform trim
for key, seq in aln.iteritems():
aln[key] = seq[trimstart:trimend]
alns.append(aln)
return alns
def __init__(self,
aln,
collapse=None,
cols=None,
color_bases=False,
seqtype=None,
show_color_bases=True,
show_bases=True,
show_labels=True,
rowspacing=None,
**options):
Track.__init__(self, **options)
self.size = [aln.alignlen(), len(aln)]
self.multiscale = Multiscale(marginx=.5, marginy=.5)
self.collapse = collapse
self.show_color_bases = show_color_bases
self.show_bases = show_bases
self.show_labels = show_labels
self.rowspacing = rowspacing
self.always_color = False
self.color_bases_vis = None
if seqtype == None:
self.seqtype = guessAlign(aln)
else:
self.seqtype = seqtype
if color_bases == True:
if self.seqtype == "dna":
self.color_bases = dna_colors
elif self.seqtype == "pep":
self.color_bases = pep_colors
else:
self.color_bases = color_bases
if collapse != None:
assert collapse in aln.keys()
cols = util.findneq('-', aln[collapse])
if cols != None:
self.aln = alignlib.subalign(aln, cols)
else:
self.aln = aln
def get_aligns(self, species, chrom, start, end,
mainspecies=lambda keys: keys[0],
collapse=False):
"""By default assumes main species is 1st sequence"""
# get records for this region
records = self.get(species, chrom, start, end)
records.sort(key=lambda x: x["start"])
# read alignments
alns = []
for record in records:
aln = fasta.read_fasta(record["filename"])
# collapse alignment
if collapse:
ind = util.findneq("-", aln[mainspecies(aln.keys())])
for key, seq in aln.iteritems():
if len(seq) != 0:
aln[key] = "".join(util.mget(seq, ind))
l2a = alignlib.local2align(aln[mainspecies(aln.keys())])
# trim front
if start > record["start"]:
trimstart = l2a[start - record["start"]]
else:
trimstart = 0
# trim end
if end < record["end"]:
trimend = l2a[-(record["end"]-end)]
else:
trimend = aln.alignlen()
# perform trim
for key, seq in aln.iteritems():
aln[key] = seq[trimstart:trimend]
alns.append(aln)
return alns
def __init__(self, aln, collapse=None, cols=None, color_bases=False,
seqtype=None, show_color_bases=True, show_bases=True,
show_labels=True,
rowspacing=None,
**options):
Track.__init__(self, **options)
self.size = [aln.alignlen(), len(aln)]
self.multiscale = Multiscale(marginx=.5, marginy=.5)
self.collapse = collapse
self.show_color_bases = show_color_bases
self.show_bases = show_bases
self.show_labels = show_labels
self.rowspacing = rowspacing
self.always_color = False
self.color_bases_vis = None
if seqtype == None:
self.seqtype = guessAlign(aln)
else:
self.seqtype = seqtype
if color_bases == True:
if self.seqtype == "dna":
self.color_bases = dna_colors
elif self.seqtype == "pep":
self.color_bases = pep_colors
else:
self.color_bases = color_bases
if collapse != None:
assert collapse in aln.keys()
cols = util.findneq('-', aln[collapse])
if cols != None:
self.aln = alignlib.subalign(aln, cols)
else:
self.aln = aln