def get_node_gtf(self):
graph_id = (
'G_%s_%d_%d_%s' %
(self.chrom, self.start, self.end, Strand.to_gtf(self.strand)))
# iterate through locus and return change point data
for n_id in self.G:
n = self.get_node_interval(n_id)
expr_data = self.get_expr_data(*n)
ref_starts = _array_subset(self.ref_start_sites, *n)
ref_stops = _array_subset(self.ref_stop_sites, *n)
# return gtf feature for each node
f = GTF.Feature()
f.seqid = self.chrom
f.source = 'taco'
f.feature = 'node'
f.start = n[0]
f.end = n[1]
f.score = 0
f.strand = Strand.to_gtf(self.strand)
f.phase = '.'
f.attrs = {
'graph_id': graph_id,
'expr_min': str(expr_data.min()),
'expr_max': str(expr_data.max()),
'expr_mean': str(expr_data.mean()),
'ref_starts': ','.join(map(str, ref_starts)),
'ref_stops': ','.join(map(str, ref_stops))
}
yield f
def get_change_point_gtf(self, cp):
graph_id = ('G_%s_%d_%d_%s' %
(self.chrom, self.start, self.end,
Strand.to_gtf(self.strand)))
features = []
f = GTF.Feature()
f.seqid = self.chrom
f.source = 'taco'
f.feature = 'changept'
f.start = cp.pos
f.end = cp.pos + 1
f.score = 0
f.strand = Strand.to_gtf(self.strand)
f.phase = '.'
f.attrs = {'graph_id': graph_id,
'sign': str(cp.sign),
'pvalue': str(cp.pvalue),
'foldchange': str(cp.foldchange)}
features.append(f)
f = GTF.Feature()
f.seqid = self.chrom
f.source = 'taco'
f.feature = 'changeinterval'
f.start = cp.start
f.end = cp.end
f.score = 0
f.strand = Strand.to_gtf(self.strand)
f.phase = '.'
f.attrs = {'graph_id': graph_id,
'sign': str(cp.sign),
'pvalue': str(cp.pvalue),
'foldchange': str(cp.foldchange)}
features.append(f)
return features
def get_change_point_gtf(self, cp):
graph_id = ('G_%s_%d_%d_%s' %
(self.chrom, self.start, self.end,
Strand.to_gtf(self.strand)))
features = []
f = GTF.Feature()
f.seqid = self.chrom
f.source = 'taco'
f.feature = 'changept'
f.start = cp.pos
f.end = cp.pos + 1
f.score = 0
f.strand = Strand.to_gtf(self.strand)
f.phase = '.'
f.attrs = {'graph_id': graph_id,
'sign': str(cp.sign),
'pvalue': str(cp.pvalue),
'foldchange': str(cp.foldchange)}
features.append(f)
f = GTF.Feature()
f.seqid = self.chrom
f.source = 'taco'
f.feature = 'changeinterval'
f.start = cp.start
f.end = cp.end
f.score = 0
f.strand = Strand.to_gtf(self.strand)
f.phase = '.'
f.attrs = {'graph_id': graph_id,
'sign': str(cp.sign),
'pvalue': str(cp.pvalue),
'foldchange': str(cp.foldchange)}
features.append(f)
return features
def get_node_gtf(self):
graph_id = ('G_%s_%d_%d_%s' %
(self.chrom, self.start, self.end,
Strand.to_gtf(self.strand)))
# iterate through locus and return change point data
for n_id in self.G.node_ids_iter():
n = self.get_node_interval(n_id)
expr_data = self.get_expr_data(*n)
ref_starts = _array_subset(self.ref_start_sites, *n)
ref_stops = _array_subset(self.ref_stop_sites, *n)
# return gtf feature for each node
f = GTF.Feature()
f.seqid = self.chrom
f.source = 'taco'
f.feature = 'node'
f.start = n[0]
f.end = n[1]
f.score = 0
f.strand = Strand.to_gtf(self.strand)
f.phase = '.'
f.attrs = {'graph_id': graph_id,
'expr_min': str(expr_data.min()),
'expr_max': str(expr_data.max()),
'expr_mean': str(expr_data.mean()),
'ref_starts': ','.join(map(str, ref_starts)),
'ref_stops': ','.join(map(str, ref_stops))}
yield f
def assemble_gene(sgraph, locus_id_str, config):
logging.debug('%s:%d-%d[%s] nodes=%d' %
(sgraph.chrom, sgraph.start, sgraph.end,
Strand.to_gtf(sgraph.strand), len(sgraph.G)))
# output splice graph node data
for f in sgraph.get_node_gtf():
print >> config.splice_graph_gtf_fh, str(f)
if config.change_point:
# detect change points
changepts = sgraph.detect_change_points(
pval=config.change_point_pvalue,
fc_cutoff=config.change_point_fold_change)
logging.debug('%s:%d-%d[%s] change points: %d' %
(sgraph.chrom, sgraph.start, sgraph.end,
Strand.to_gtf(sgraph.strand), len(changepts)))
for cp in changepts:
sgraph.apply_change_point(cp, config.change_point_trim)
# output splice graph change points
for f in sgraph.get_change_point_gtf(cp):
print >> config.splice_graph_gtf_fh, str(f)
# must recreate splice graph after finding change points
if len(changepts) > 0:
sgraph.recreate()
# run isoform path finding algorithm, filter and group into genes
for gene_isoforms in assemble_isoforms(sgraph, config):
# assign gene_id and tss_id
assign_ids(gene_isoforms, sgraph.strand, config.gene_id_value_obj,
config.tss_id_value_obj)
# write output
for isoform in gene_isoforms:
# assign transcript id
t_id = config.t_id_value_obj.next()
# get strings for each id
t_id_str = "TU%d" % t_id
tss_id_str = "TSS%d" % (isoform.tss_id)
gene_id_str = "G%d" % (isoform.gene_id)
# write to GTF
for f in get_gtf_features(chrom=sgraph.chrom,
strand=sgraph.strand,
exons=isoform.path,
locus_id=locus_id_str,
gene_id=gene_id_str,
tss_id=tss_id_str,
transcript_id=t_id_str,
expr=isoform.expr,
rel_frac=isoform.rel_frac,
abs_frac=isoform.abs_frac):
print >> config.assembly_gtf_fh, str(f)
# write to BED
name = "%s|%s(%.1f)" % (gene_id_str, t_id_str, isoform.expr)
fields = write_bed(sgraph.chrom, name, sgraph.strand,
int(round(1000.0 * isoform.rel_frac)),
isoform.path)
print >> config.assembly_bed_fh, '\t'.join(fields)
def assemble_gene(sgraph, locus_id_str, config):
logging.debug('%s:%d-%d[%s] nodes=%d' %
(sgraph.chrom, sgraph.start, sgraph.end,
Strand.to_gtf(sgraph.strand), len(sgraph.G)))
# output splice graph node data
for f in sgraph.get_node_gtf():
print >>config.splice_graph_gtf_fh, str(f)
if config.change_point:
# detect change points
changepts = sgraph.detect_change_points(
pval=config.change_point_pvalue,
fc_cutoff=config.change_point_fold_change)
logging.debug('%s:%d-%d[%s] change points: %d' %
(sgraph.chrom, sgraph.start, sgraph.end,
Strand.to_gtf(sgraph.strand), len(changepts)))
for cp in changepts:
sgraph.apply_change_point(cp, config.change_point_trim)
# output splice graph change points
for f in sgraph.get_change_point_gtf(cp):
print >>config.splice_graph_gtf_fh, str(f)
# must recreate splice graph after finding change points
if len(changepts) > 0:
sgraph.recreate()
# run isoform path finding algorithm, filter and group into genes
for gene_isoforms in assemble_isoforms(sgraph, config):
# assign gene_id and tss_id
assign_ids(gene_isoforms, sgraph.strand, config.gene_id_value_obj,
config.tss_id_value_obj)
# write output
for isoform in gene_isoforms:
# assign transcript id
t_id = config.t_id_value_obj.next()
# get strings for each id
t_id_str = "TU%d" % t_id
tss_id_str = "TSS%d" % (isoform.tss_id)
gene_id_str = "G%d" % (isoform.gene_id)
# write to GTF
for f in get_gtf_features(chrom=sgraph.chrom,
strand=sgraph.strand,
exons=isoform.path,
locus_id=locus_id_str,
gene_id=gene_id_str,
tss_id=tss_id_str,
transcript_id=t_id_str,
expr=isoform.expr,
rel_frac=isoform.rel_frac,
abs_frac=isoform.abs_frac):
print >>config.assembly_gtf_fh, str(f)
# write to BED
name = "%s|%s(%.1f)" % (gene_id_str, t_id_str, isoform.expr)
fields = write_bed(sgraph.chrom, name, sgraph.strand,
int(round(1000.0 * isoform.rel_frac)),
isoform.path)
print >>config.assembly_bed_fh, '\t'.join(fields)
def to_gtf(self):
strand_str = Strand.to_gtf(self.strand)
f = GTF.Feature()
f.seqid = self.chrom
f.source = 'taco'
f.feature = 'transcript'
f.start = self.start
f.end = self.end
f.score = 0.0
f.strand = strand_str
f.phase = '.'
f.attrs = {GTF.Attr.TRANSCRIPT_ID: self._id,
GTF.Attr.SAMPLE_ID: self.sample_id,
GTF.Attr.EXPR: str(self.expr),
GTF.Attr.REF: str(int(self.is_ref))}
yield f
for e in self.exons:
f = GTF.Feature()
f.seqid = self.chrom
f.source = 'taco'
f.feature = 'exon'
f.start = e.start
f.end = e.end
f.score = 0.0
f.strand = strand_str
f.phase = '.'
f.attrs = {GTF.Attr.TRANSCRIPT_ID: self._id}
yield f
def to_gtf(self):
strand_str = Strand.to_gtf(self.strand)
f = GTF.Feature()
f.seqid = self.chrom
f.source = 'taco'
f.feature = 'transcript'
f.start = self.start
f.end = self.end
f.score = 0.0
f.strand = strand_str
f.phase = '.'
f.attrs = {
GTF.Attr.TRANSCRIPT_ID: self._id,
GTF.Attr.SAMPLE_ID: self.sample_id,
GTF.Attr.EXPR: str(self.expr),
GTF.Attr.REF: str(int(self.is_ref))
}
yield f
for e in self.exons:
f = GTF.Feature()
f.seqid = self.chrom
f.source = 'taco'
f.feature = 'exon'
f.start = e.start
f.end = e.end
f.score = 0.0
f.strand = strand_str
f.phase = '.'
f.attrs = {GTF.Attr.TRANSCRIPT_ID: self._id}
yield f
def create_optimal_path_graph(sgraph,
kmax=0,
loss_threshold=0.10,
stats_fh=None):
'''
create a path graph from the original splice graph using paths of length
'k' for assembly. The parameter 'k' will be chosen by maximizing the
number of reachable k-mers in the path graph while tolerating at most
'loss_threshold' percent of expression.
'''
# find upper bound to k
user_kmax = kmax
kmax = find_longest_path(sgraph)
if user_kmax > 0:
# user can force a specific kmax (for debugging/testing purposes)
kmax = min(user_kmax, kmax)
sgraph_id_str = '%s:%d-%d[%s]' % (sgraph.chrom, sgraph.start, sgraph.end,
Strand.to_gtf(sgraph.strand))
tot_expr = sum(sgraph.get_node_expr_data(n).mean() for n in sgraph.G)
def compute_kmers(k):
K = create_path_graph(sgraph, k)
valid = K.graph['valid']
short_transfrags = K.graph['short_transfrags']
num_lost_kmers = K.graph['num_lost_kmers']
lost_nodes = get_lost_nodes(sgraph, K)
lost_expr = sum(
sgraph.get_node_expr_data(n).mean() for n in lost_nodes)
lost_expr_frac = 0.0 if tot_expr == 0 else lost_expr / tot_expr
logging.debug('%s k=%d kmax=%d t=%d kmers=%d short_transfrags=%d '
'lost_kmers=%d tot_expr=%.3f lost_expr=%.3f '
'lost_expr_frac=%.3f valid=%d' %
(sgraph_id_str, k, kmax, len(sgraph.transfrags), len(K),
len(short_transfrags), num_lost_kmers, tot_expr,
lost_expr, lost_expr_frac, int(valid)))
if stats_fh:
fields = [
sgraph_id_str, k, kmax,
len(sgraph.transfrags),
len(K),
len(short_transfrags), num_lost_kmers, tot_expr, lost_expr,
lost_expr_frac,
int(valid)
]
print >> stats_fh, '\t'.join(map(str, fields))
if not valid:
return -k
#if lost_expr_frac > loss_threshold:
# return -k
return len(K)
k, num_kmers = maximize_bisect(compute_kmers, 1, kmax, 0)
logging.debug('Creating path graph k=%d num_kmers=%d' % (k, num_kmers))
K = create_path_graph(sgraph, k)
logging.debug('Rescuing short transfrags')
rescue_short_transfrags_saindex(K)
return K, k
def from_gtf(f):
'''GTF.Feature object to Transfrag'''
return Transfrag(chrom=f.seqid,
strand=Strand.from_gtf(f.strand),
_id=f.attrs[GTF.Attr.TRANSCRIPT_ID],
sample_id=f.attrs.get(GTF.Attr.SAMPLE_ID, None),
expr=float(f.attrs.get(GTF.Attr.EXPR, 0.0)),
is_ref=bool(int(f.attrs.get(GTF.Attr.REF, '0'))),
exons=None)
def from_gtf(f):
'''GTF.Feature object to Transfrag'''
return Transfrag(chrom=f.seqid,
strand=Strand.from_gtf(f.strand),
_id=f.attrs[GTF.Attr.TRANSCRIPT_ID],
sample_id=f.attrs.get(GTF.Attr.SAMPLE_ID, None),
expr=float(f.attrs.get(GTF.Attr.EXPR, 0.0)),
is_ref=bool(int(f.attrs.get(GTF.Attr.REF, '0'))),
exons=None)
def get_stats(self, K, kmax=None, lost_short=0, lost_short_expr=0.0, is_opt=0):
if kmax is None:
kmax = self.longest_path_length
expr_frac = 0.0 if self.total_expr == 0 else K.graph_expr / self.total_expr
opt = int(round(expr_frac * len(K)))
fields = [self.chrom, self.start, self.end, Strand.to_gtf(self.strand),
K.k, kmax, len(self.paths), len(K.short_transfrags),
K.short_expr, lost_short, lost_short_expr,
len(K), K.num_lost_kmers, self.total_expr, K.graph_expr,
expr_frac, int(K.valid), opt, is_opt]
return fields
def create_optimal(self, kmax=0, loss_threshold=0.10, stats_fh=None):
'''
create a graph where nodes are paths of length 'k'. the parameter
'k' is chosen to maximizing the number of reachable k-mers in the
path graph while tolerating at most 'loss_threshold' percent of
expression.
'''
if len(self.paths) == 0:
return None, 0
# find upper bound to k
user_kmax = kmax
kmax = self.longest_path_length()
if user_kmax > 0:
# user can force a specific kmax (for debugging/testing purposes)
kmax = min(user_kmax, kmax)
id_str = (
'%s:%d-%d[%s]' %
(self.chrom, self.start, self.end, Strand.to_gtf(self.strand)))
def compute_kmers(k):
K = self.create(k)
tot_expr = sum(K.exprs[i] for i in K.node_ids_iter())
lost_expr = K.lost_kmer_expr
lost_expr_frac = 0.0 if tot_expr == 0 else lost_expr / tot_expr
if stats_fh:
fields = [
self.chrom, self.start, self.end,
Strand.to_gtf(self.strand), k, kmax,
len(self.paths), K.n,
len(K.short_transfrags), K.num_lost_kmers, tot_expr,
lost_expr, lost_expr_frac,
int(K.valid)
]
print >> stats_fh, '\t'.join(map(str, fields))
if not K.valid:
return -k
#if lost_expr_frac > loss_threshold:
# return -k
return len(K)
k, num_kmers = maximize_bisect(compute_kmers, 1, kmax, 0)
logging.debug('%s creating path graph k=%d num_kmers=%d' %
(id_str, k, num_kmers))
K = self.create(k)
logging.debug('%s rescuing short transfrags kmers=%d' %
(id_str, len(K)))
num_lost = self.rescue_short_transfrags(K, K.short_transfrags)
logging.debug('%s lost %d of %d short transfrags' %
(id_str, num_lost, len(K.short_transfrags)))
return K, k
def parse_gtf(gtf_iter, sample_id, gtf_expr_attr, is_ref):
'''
returns list of Transfrag objects
'''
t_dict = collections.OrderedDict()
total_expr = 0.0
cur_t_id = 1
for gtf_line in gtf_iter:
if not gtf_line:
continue
if not gtf_line.strip():
continue
if gtf_line.startswith("#"):
continue
f = GTF.Feature.from_str(gtf_line)
if f.feature == 'transcript':
t_id = f.attrs[GTF.Attr.TRANSCRIPT_ID]
if t_id in t_dict:
raise GTFError("Transcript '%s' duplicate detected" % t_id)
# rename transcript id
new_t_id = "%s.%d" % (sample_id, cur_t_id)
cur_t_id += 1
# parse expression
if is_ref:
expr = 0.0
else:
if gtf_expr_attr not in f.attrs:
raise GTFError("GTF expression attribute '%s' not found" %
(gtf_expr_attr))
expr = float(f.attrs[gtf_expr_attr])
total_expr += expr
# create transfrag
t = Transfrag(chrom=f.seqid,
strand=Strand.from_gtf(f.strand),
_id=new_t_id,
expr=float(expr),
is_ref=is_ref,
exons=None)
t_dict[t_id] = t
elif f.feature == 'exon':
t_id = f.attrs[GTF.Attr.TRANSCRIPT_ID]
if t_id not in t_dict:
logging.error('Feature: "%s"' % str(f))
raise GTFError("Transcript '%s' exon feature appeared in "
"gtf file prior to transcript feature" %
t_id)
t = t_dict[t_id]
t.exons.append(Exon(f.start, f.end))
return t_dict.values(), total_expr
def create_optimal_path_graph(sgraph, kmax=0, loss_threshold=0.10,
stats_fh=None):
'''
create a path graph from the original splice graph using paths of length
'k' for assembly. The parameter 'k' will be chosen by maximizing the
number of reachable k-mers in the path graph while tolerating at most
'loss_threshold' percent of expression.
'''
# find upper bound to k
user_kmax = kmax
kmax = find_longest_path(sgraph)
if user_kmax > 0:
# user can force a specific kmax (for debugging/testing purposes)
kmax = min(user_kmax, kmax)
sgraph_id_str = '%s:%d-%d[%s]' % (sgraph.chrom, sgraph.start, sgraph.end,
Strand.to_gtf(sgraph.strand))
tot_expr = sum(sgraph.get_node_expr_data(n).mean() for n in sgraph.G)
def compute_kmers(k):
K = create_path_graph(sgraph, k)
valid = K.graph['valid']
short_transfrags = K.graph['short_transfrags']
num_lost_kmers = K.graph['num_lost_kmers']
lost_nodes = get_lost_nodes(sgraph, K)
lost_expr = sum(sgraph.get_node_expr_data(n).mean() for n in lost_nodes)
lost_expr_frac = 0.0 if tot_expr == 0 else lost_expr / tot_expr
logging.debug('%s k=%d kmax=%d t=%d kmers=%d short_transfrags=%d '
'lost_kmers=%d tot_expr=%.3f lost_expr=%.3f '
'lost_expr_frac=%.3f valid=%d' %
(sgraph_id_str, k, kmax, len(sgraph.transfrags),
len(K), len(short_transfrags), num_lost_kmers,
tot_expr, lost_expr, lost_expr_frac, int(valid)))
if stats_fh:
fields = [sgraph_id_str, k, kmax, len(sgraph.transfrags), len(K),
len(short_transfrags), num_lost_kmers, tot_expr,
lost_expr, lost_expr_frac, int(valid)]
print >>stats_fh, '\t'.join(map(str, fields))
if not valid:
return -k
#if lost_expr_frac > loss_threshold:
# return -k
return len(K)
k, num_kmers = maximize_bisect(compute_kmers, 1, kmax, 0)
logging.debug('Creating path graph k=%d num_kmers=%d' % (k, num_kmers))
K = create_path_graph(sgraph, k)
logging.debug('Rescuing short transfrags')
rescue_short_transfrags_saindex(K)
return K, k
def write_splice_bed(self, fh):
intron_dict = collections.defaultdict(float)
for strand in Strand.POS, Strand.NEG:
for t in self.strand_transfrags[strand]:
if t.is_ref:
continue
for start, end in t.iterintrons():
intron_dict[(start, end, strand)] += t.expr
for intron, expr in intron_dict.iteritems():
start, end, strand = intron
fields = [self.chrom, str(start - 1), str(end + 1), 'JUNC',
str(expr), Strand.to_gtf(strand),
str(start - 1), str(end + 1), '255,0,0',
'2', '1,1', '0,%d' % (end + 1 - start)]
print >>fh, '\t'.join(fields)
def write_splice_bed(self, fh):
intron_dict = collections.defaultdict(float)
for strand in Strand.POS, Strand.NEG:
for t in self.strand_transfrags[strand]:
if t.is_ref:
continue
for start, end in t.iterintrons():
intron_dict[(start, end, strand)] += t.expr
for intron, expr in intron_dict.iteritems():
start, end, strand = intron
fields = [self.chrom, str(start - 1), str(end + 1), 'JUNC',
str(expr), Strand.to_gtf(strand),
str(start - 1), str(end + 1), '255,0,0',
'2', '1,1', '0,%d' % (end + 1 - start)]
print >>fh, '\t'.join(fields)
def parse_gtf(gtf_iter, sample_id, gtf_expr_attr, is_ref):
'''
returns list of Transfrag objects
'''
t_dict = collections.OrderedDict()
total_expr = 0.0
cur_t_id = 1
for gtf_line in gtf_iter:
if not gtf_line:
continue
if not gtf_line.strip():
continue
if gtf_line.startswith("#"):
continue
f = GTF.Feature.from_str(gtf_line)
if f.feature == 'transcript':
t_id = f.attrs[GTF.Attr.TRANSCRIPT_ID]
if t_id in t_dict:
raise GTFError("Transcript '%s' duplicate detected" % t_id)
# rename transcript id
new_t_id = "%s.%d" % (sample_id, cur_t_id)
cur_t_id += 1
# parse expression
if is_ref:
expr = 0.0
else:
if gtf_expr_attr not in f.attrs:
raise GTFError("GTF expression attribute '%s' not found" %
(gtf_expr_attr))
expr = float(f.attrs[gtf_expr_attr])
total_expr += expr
# create transfrag
t = Transfrag(chrom=f.seqid,
strand=Strand.from_gtf(f.strand),
_id=new_t_id,
expr=float(expr),
is_ref=is_ref,
exons=None)
t_dict[t_id] = t
elif f.feature == 'exon':
t_id = f.attrs[GTF.Attr.TRANSCRIPT_ID]
if t_id not in t_dict:
logging.error('Feature: "%s"' % str(f))
raise GTFError("Transcript '%s' exon feature appeared in "
"gtf file prior to transcript feature" % t_id)
t = t_dict[t_id]
t.exons.append(Exon(f.start, f.end))
return t_dict.values(), total_expr
def create_optimal(self, kmax=0, loss_threshold=0.10, stats_fh=None):
'''
create a graph where nodes are paths of length 'k'. the parameter
'k' is chosen to maximizing the number of reachable k-mers in the
path graph while tolerating at most 'loss_threshold' percent of
expression.
'''
if len(self.paths) == 0:
return None, 0
# find upper bound to k
user_kmax = kmax
kmax = self.longest_path_length()
if user_kmax > 0:
# user can force a specific kmax (for debugging/testing purposes)
kmax = min(user_kmax, kmax)
id_str = ('%s:%d-%d[%s]' % (self.chrom, self.start, self.end,
Strand.to_gtf(self.strand)))
def compute_kmers(k):
K = self.create(k)
tot_expr = sum(K.exprs[i] for i in K.node_ids_iter())
lost_expr = K.lost_kmer_expr
lost_expr_frac = 0.0 if tot_expr == 0 else lost_expr / tot_expr
if stats_fh:
fields = [self.chrom, self.start, self.end,
Strand.to_gtf(self.strand), k, kmax,
len(self.paths), K.n, len(K.short_transfrags),
K.num_lost_kmers, tot_expr, lost_expr,
lost_expr_frac, int(K.valid)]
print >>stats_fh, '\t'.join(map(str, fields))
if not K.valid:
return -k
#if lost_expr_frac > loss_threshold:
# return -k
return len(K)
k, num_kmers = maximize_bisect(compute_kmers, 1, kmax, 0)
logging.debug('%s creating path graph k=%d num_kmers=%d' %
(id_str, k, num_kmers))
K = self.create(k)
logging.debug('%s rescuing short transfrags kmers=%d' %
(id_str, len(K)))
num_lost = self.rescue_short_transfrags(K, K.short_transfrags)
logging.debug('%s lost %d of %d short transfrags' %
(id_str, num_lost, len(K.short_transfrags)))
return K, k
def compute_kmers(k):
K = self.create(k)
tot_expr = sum(K.exprs[i] for i in K.node_ids_iter())
lost_expr = K.lost_kmer_expr
lost_expr_frac = 0.0 if tot_expr == 0 else lost_expr / tot_expr
if stats_fh:
fields = [self.chrom, self.start, self.end,
Strand.to_gtf(self.strand), k, kmax,
len(self.paths), K.n, len(K.short_transfrags),
K.num_lost_kmers, tot_expr, lost_expr,
lost_expr_frac, int(K.valid)]
print >>stats_fh, '\t'.join(map(str, fields))
if not K.valid:
return -k
#if lost_expr_frac > loss_threshold:
# return -k
return len(K)
def get_stats(self,
K,
kmax=None,
lost_short=0,
lost_short_expr=0.0,
is_opt=0):
if kmax is None:
kmax = self.longest_path_length
expr_frac = 0.0 if self.total_expr == 0 else K.graph_expr / self.total_expr
opt = int(round(expr_frac * len(K)))
fields = [
self.chrom, self.start, self.end,
Strand.to_gtf(self.strand), K.k, kmax,
len(self.paths),
len(K.short_transfrags), K.short_expr, lost_short, lost_short_expr,
len(K), K.num_lost_kmers, self.total_expr, K.graph_expr, expr_frac,
int(K.valid), opt, is_opt
]
return fields
def to_bed(self):
tx_start = self.exons[0].start
tx_end = self.exons[-1].end
block_sizes = []
block_starts = []
for e in self.exons:
block_starts.append(e.start - tx_start)
block_sizes.append(e.end - e.start)
# make bed fields
fields = [
self.chrom,
str(tx_start),
str(tx_end), self._id,
str(self.expr),
Strand.to_gtf(self.strand), '0', '0', '0',
str(len(self.exons)), ','.join(map(str, block_sizes)),
','.join(map(str, block_starts))
]
return fields
def compute_kmers(k):
K = self.create(k)
tot_expr = sum(K.exprs[i] for i in K.node_ids_iter())
lost_expr = K.lost_kmer_expr
lost_expr_frac = 0.0 if tot_expr == 0 else lost_expr / tot_expr
if stats_fh:
fields = [
self.chrom, self.start, self.end,
Strand.to_gtf(self.strand), k, kmax,
len(self.paths), K.n,
len(K.short_transfrags), K.num_lost_kmers, tot_expr,
lost_expr, lost_expr_frac,
int(K.valid)
]
print >> stats_fh, '\t'.join(map(str, fields))
if not K.valid:
return -k
#if lost_expr_frac > loss_threshold:
# return -k
return len(K)
def get_gtf_features(chrom, strand, exons, locus_id, gene_id, tss_id,
transcript_id, expr, rel_frac, abs_frac):
tx_start = exons[0].start
tx_end = exons[-1].end
strand_str = Strand.to_gtf(strand)
attr_dict = {
'locus_id': locus_id,
'gene_id': gene_id,
'tss_id': tss_id,
'transcript_id': transcript_id
}
f = GTF.Feature()
f.seqid = chrom
f.source = 'taco'
f.feature = 'transcript'
f.start = tx_start
f.end = tx_end
f.score = int(round(1000.0 * rel_frac))
f.strand = strand_str
f.phase = '.'
f.attrs = {
'expr': '%.3f' % expr,
'rel_frac': '%.5f' % rel_frac,
'abs_frac': '%.5f' % abs_frac
}
f.attrs.update(attr_dict)
yield f
for e in exons:
f = GTF.Feature()
f.seqid = chrom
f.source = 'taco'
f.feature = 'exon'
f.start = e.start
f.end = e.end
f.score = int(round(1000.0 * rel_frac))
f.strand = strand_str
f.phase = '.'
f.attrs = {}
f.attrs.update(attr_dict)
yield f
def from_bed(line):
fields = line.strip().split('\t')
chrom = fields[0]
tx_start = int(fields[1])
_id = fields[3]
is_ref = (_id.split('.')[0] == Sample.REF_ID)
expr = float(fields[4])
strand = Strand.from_bed(fields[5])
num_exons = int(fields[9])
block_sizes = fields[10].split(',')
block_starts = fields[11].split(',')
exons = []
for i in xrange(num_exons):
start = tx_start + int(block_starts[i])
end = start + int(block_sizes[i])
exons.append(Exon(start, end))
return Transfrag(chrom=chrom,
strand=strand,
_id=_id,
expr=expr,
is_ref=is_ref,
exons=exons)
def detect_change_points(self, *args, **kwargs):
'''
*args, **kwargs: passed directly to 'run_changepoint'
returns list of ChangePoint tuples
'''
changepts = []
for n_id in self.G:
n = self.get_node_interval(n_id)
expr_data = self.get_expr_data(n.start, n.end)
for cp in run_changepoint(expr_data, *args, **kwargs):
# add offset from start of node to change point positions
cp = cp._replace(pos=n.start + cp.pos,
start=n.start + cp.start,
end=n.start + cp.end)
changepts.append(cp)
logging.debug(
'\t%s:%d-%d[%s] node: %s-%s cp:%d(%d-%d) '
'p=%.3f fc=%.3f' %
(self.chrom, self.start, self.end,
Strand.to_gtf(self.strand), n.start, n.end, cp.pos,
cp.start, cp.end, cp.pvalue, cp.foldchange))
return changepts
def detect_change_points(self, *args, **kwargs):
'''
*args, **kwargs: passed directly to 'run_changepoint'
returns list of ChangePoint tuples
'''
genome_id_str = ('%s:%d-%d[%s]' % (self.chrom, self.start, self.end,
Strand.to_gtf(self.strand)))
changepts = []
for n in self.G.nodes_iter():
expr_data = self.get_expr_data(*n)
for cp in run_changepoint(expr_data, *args, **kwargs):
# add offset from start of node to change point positions
cp = cp._replace(pos=n.start + cp.pos,
start=n.start + cp.start,
end=n.start + cp.end)
changepts.append(cp)
logging.debug('%s changepoint node=(%s-%s) '
'pos=%d interval=(%d-%d) p=%.3f fc=%.3f' %
(genome_id_str, n.start,
n.end, cp.pos, cp.start, cp.end,
cp.pvalue, cp.foldchange))
return changepts
def detect_change_points(self, *args, **kwargs):
'''
*args, **kwargs: passed directly to 'run_changepoint'
returns list of ChangePoint tuples
'''
genome_id_str = (
'%s:%d-%d[%s]' %
(self.chrom, self.start, self.end, Strand.to_gtf(self.strand)))
changepts = []
for n in self.G.nodes_iter():
expr_data = self.get_expr_data(*n)
for cp in run_changepoint(expr_data, *args, **kwargs):
# add offset from start of node to change point positions
cp = cp._replace(pos=n.start + cp.pos,
start=n.start + cp.start,
end=n.start + cp.end)
changepts.append(cp)
logging.debug('%s changepoint node=(%s-%s) '
'pos=%d interval=(%d-%d) p=%.3f fc=%.3f' %
(genome_id_str, n.start, n.end, cp.pos, cp.start,
cp.end, cp.pvalue, cp.foldchange))
return changepts
def detect_change_points(self, *args, **kwargs):
'''
*args, **kwargs: passed directly to 'run_changepoint'
returns list of ChangePoint tuples
'''
changepts = []
for n_id in self.G:
n = self.get_node_interval(n_id)
expr_data = self.get_expr_data(n.start, n.end)
for cp in run_changepoint(expr_data, *args, **kwargs):
# add offset from start of node to change point positions
cp = cp._replace(pos=n.start + cp.pos,
start=n.start + cp.start,
end=n.start + cp.end)
changepts.append(cp)
logging.debug('\t%s:%d-%d[%s] node: %s-%s cp:%d(%d-%d) '
'p=%.3f fc=%.3f' %
(self.chrom, self.start, self.end,
Strand.to_gtf(self.strand), n.start,
n.end, cp.pos, cp.start, cp.end,
cp.pvalue, cp.foldchange))
return changepts
def get_gtf_features(chrom, strand, exons, locus_id, gene_id, tss_id,
transcript_id, expr, rel_frac, abs_frac):
tx_start = exons[0].start
tx_end = exons[-1].end
strand_str = Strand.to_gtf(strand)
attr_dict = {'locus_id': locus_id,
'gene_id': gene_id,
'tss_id': tss_id,
'transcript_id': transcript_id}
f = GTF.Feature()
f.seqid = chrom
f.source = 'taco'
f.feature = 'transcript'
f.start = tx_start
f.end = tx_end
f.score = int(round(1000.0 * rel_frac))
f.strand = strand_str
f.phase = '.'
f.attrs = {'expr': '%.3f' % expr,
'rel_frac': '%.5f' % rel_frac,
'abs_frac': '%.5f' % abs_frac}
f.attrs.update(attr_dict)
yield f
for e in exons:
f = GTF.Feature()
f.seqid = chrom
f.source = 'taco'
f.feature = 'exon'
f.start = e.start
f.end = e.end
f.score = int(round(1000.0 * rel_frac))
f.strand = strand_str
f.phase = '.'
f.attrs = {}
f.attrs.update(attr_dict)
yield f
def write_bed(chrom, name, strand, score, exons):
assert all(exons[0].start < x.start for x in exons[1:])
assert all(exons[-1].end > x.end for x in exons[:-1])
tx_start = exons[0].start
tx_end = exons[-1].end
block_sizes = []
block_starts = []
for e in exons:
block_starts.append(e.start - tx_start)
block_sizes.append(e.end - e.start)
# make bed fields
fields = [chrom,
str(tx_start),
str(tx_end),
str(name),
str(score),
Strand.to_gtf(strand),
str(tx_start),
str(tx_start),
'0',
str(len(exons)),
','.join(map(str, block_sizes)) + ',',
','.join(map(str, block_starts)) + ',']
return fields
def write_bed(chrom, name, strand, score, exons):
assert all(exons[0].start < x.start for x in exons[1:])
assert all(exons[-1].end > x.end for x in exons[:-1])
tx_start = exons[0].start
tx_end = exons[-1].end
block_sizes = []
block_starts = []
for e in exons:
block_starts.append(e.start - tx_start)
block_sizes.append(e.end - e.start)
# make bed fields
fields = [
chrom,
str(tx_start),
str(tx_end),
str(name),
str(score),
Strand.to_gtf(strand),
str(tx_start),
str(tx_start), '0',
str(len(exons)), ','.join(map(str, block_sizes)) + ',',
','.join(map(str, block_starts)) + ','
]
return fields
def __str__(self):
return ('PathGraphFactory %s:%d-%d[%s]' %
(self.chrom, self.start, self.end, Strand.to_gtf(self.strand)))
def __str__(self):
return ('SpliceGraph %s:%d-%d[%s] transfrags: %d' %
(self.chrom, self.start, self.end, Strand.to_gtf(
self.strand), len(self.transfrags)))
def __str__(self):
return ('SpliceGraph %s:%d-%d[%s] transfrags: %d' %
(self.chrom, self.start, self.end,
Strand.to_gtf(self.strand), len(self.transfrags)))
def assemble_isoforms(sgraph, config):
# create a path graph from the splice graph
K, k = create_optimal_path_graph(
sgraph,
kmax=config.path_graph_kmax,
loss_threshold=config.path_graph_loss_threshold,
stats_fh=config.path_graph_stats_fh)
if K is None:
return []
if len(K) == 0:
return []
# report lost nodes
if config.assembly_loss_gtf_fh is not None:
graph_id = ('L_%s:%d-%d[%s]' % (sgraph.chrom, sgraph.start, sgraph.end,
Strand.to_gtf(sgraph.strand)))
for n_id in get_lost_nodes(sgraph, K):
n = sgraph.get_node_interval(n_id)
expr_data = sgraph.get_node_expr_data(n_id)
# return gtf feature for each node
f = GTF.Feature()
f.seqid = sgraph.chrom
f.source = 'taco'
f.feature = 'lost_node'
f.start = n[0]
f.end = n[1]
f.score = 0.0
f.strand = Strand.to_gtf(sgraph.strand)
f.phase = '.'
f.attrs = {'graph_id': graph_id, 'expr': str(expr_data.mean())}
print >> config.assembly_loss_gtf_fh, str(f)
# smooth kmer graph
smooth_graph(K)
source_node = K.graph['source']
source_expr = K.node[source_node][KMER_EXPR]
logging.debug('%s:%d-%d[%s] finding paths in k=%d graph '
'(%d nodes) source_expr=%f' %
(sgraph.chrom, sgraph.start, sgraph.end,
Strand.to_gtf(sgraph.strand), k, len(K), source_expr))
id_kmer_map = K.graph['id_kmer_map']
paths = []
for kmer_path, expr in find_paths(K, KMER_EXPR, config.path_frac,
config.max_paths):
path = reconstruct_path(kmer_path, id_kmer_map, sgraph)
logging.debug("\texpr=%f length=%d" % (expr, len(path)))
paths.append((path, expr))
# build gene clusters
clusters, filtered = Cluster.build(paths, min_frac=config.isoform_frac)
logging.debug('\tclusters: %d filtered: %d' %
(len(clusters), len(filtered)))
gene_isoforms = []
for cluster in clusters:
isoforms = []
for path, expr, rel_frac, abs_frac in cluster.iterpaths():
isoforms.append(
Isoform(path=path,
expr=expr,
rel_frac=rel_frac,
abs_frac=abs_frac))
# apply max isoforms limit (per cluster)
if config.max_isoforms > 0:
isoforms = isoforms[:config.max_isoforms]
gene_isoforms.append(isoforms)
return gene_isoforms
def __str__(self):
return ('PathGraphFactory %s:%d-%d[%s]' %
(self.chrom, self.start, self.end, Strand.to_gtf(self.strand)))
def assemble_isoforms(sgraph, config):
# create a path graph from the splice graph
K, k = create_optimal_path_graph(
sgraph,
kmax=config.path_graph_kmax,
loss_threshold=config.path_graph_loss_threshold,
stats_fh=config.path_graph_stats_fh)
if K is None:
return []
if len(K) == 0:
return []
# report lost nodes
if config.assembly_loss_gtf_fh is not None:
graph_id = ('L_%s:%d-%d[%s]' %
(sgraph.chrom, sgraph.start, sgraph.end,
Strand.to_gtf(sgraph.strand)))
for n_id in get_lost_nodes(sgraph, K):
n = sgraph.get_node_interval(n_id)
expr_data = sgraph.get_node_expr_data(n_id)
# return gtf feature for each node
f = GTF.Feature()
f.seqid = sgraph.chrom
f.source = 'taco'
f.feature = 'lost_node'
f.start = n[0]
f.end = n[1]
f.score = 0.0
f.strand = Strand.to_gtf(sgraph.strand)
f.phase = '.'
f.attrs = {'graph_id': graph_id,
'expr': str(expr_data.mean())}
print >>config.assembly_loss_gtf_fh, str(f)
# smooth kmer graph
smooth_graph(K)
source_node = K.graph['source']
source_expr = K.node[source_node][KMER_EXPR]
logging.debug('%s:%d-%d[%s] finding paths in k=%d graph '
'(%d nodes) source_expr=%f' %
(sgraph.chrom, sgraph.start, sgraph.end,
Strand.to_gtf(sgraph.strand), k, len(K),
source_expr))
id_kmer_map = K.graph['id_kmer_map']
paths = []
for kmer_path, expr in find_paths(K, KMER_EXPR, config.path_frac,
config.max_paths):
path = reconstruct_path(kmer_path, id_kmer_map, sgraph)
logging.debug("\texpr=%f length=%d" % (expr, len(path)))
paths.append((path, expr))
# build gene clusters
clusters, filtered = Cluster.build(paths, min_frac=config.isoform_frac)
logging.debug('\tclusters: %d filtered: %d' %
(len(clusters), len(filtered)))
gene_isoforms = []
for cluster in clusters:
isoforms = []
for path, expr, rel_frac, abs_frac in cluster.iterpaths():
isoforms.append(Isoform(path=path, expr=expr, rel_frac=rel_frac,
abs_frac=abs_frac))
# apply max isoforms limit (per cluster)
if config.max_isoforms > 0:
isoforms = isoforms[:config.max_isoforms]
gene_isoforms.append(isoforms)
return gene_isoforms