def test_empty_graph_bug():
t_dict, locus = read_single_locus('empty_graph_bug.gtf')
transfrags = locus.get_transfrags(Strand.POS)
sgraph = SpliceGraph.create(transfrags)
pgf = PathGraphFactory(sgraph)
K, k = pgf.create_optimal()
assert K is None
def test_path2():
t_dict, locus = read_single_locus('noc2l_locus.gtf')
for sgraph in locus.create_splice_graphs():
pgraphfactory = PathGraphFactory(sgraph)
pgraph, k = pgraphfactory.create_optimal()
paths = find_paths(pgraph)
return
def test_path1():
t_dict, locus = read_single_locus('path1.gtf')
transfrags = locus.get_transfrags(Strand.POS)
sgraph = SpliceGraph.create(transfrags)
k = 2
pgf = PathGraphFactory(sgraph)
pgraph = pgf.create(k)
paths = find_paths(pgraph)
return
def test_path_graph_factory():
t_dict, locus = read_single_locus('path1.gtf')
sgraph = SpliceGraph.create(t_dict.values())
pgraphfactory = PathGraphFactory(sgraph)
g1 = pgraphfactory.create(k=1)
assert len(g1) == 5
g2 = pgraphfactory.create(k=2)
assert len(g2) == 6
gopt, k = pgraphfactory.create_optimal()
assert k == 2
return
def test_topological_sort():
G = Graph()
G.add_path((G.SOURCE, 10, 20, 30, 40, G.SINK))
G.add_path((G.SOURCE, 10, 30, 40, G.SINK))
G.add_path((G.SOURCE, 10, G.SINK))
G.add_path((G.SOURCE, 20, G.SINK))
assert G.is_topological_sort(G.topological_sort())
t_dict, locus = read_single_locus('noc2l_locus.gtf')
for sgraph in locus.create_splice_graphs():
pgf = PathGraphFactory(sgraph)
G = pgf.create(k=1)
assert G.is_topological_sort(G.topological_sort())
assert G.is_topological_sort(G.topological_sort_dfs())
def test_ccle55_cuff_noc2l():
'''Locus containing from 55 CCLE samples assembled with Cufflinks'''
# pull SpliceGraph out of GTF
t_dict, locus = read_single_locus('noc2l_locus.gtf')
found_sgraph = False
for sgraph in locus.create_splice_graphs():
if (sgraph.chrom == 'chr1' and sgraph.start == 934942 and
sgraph.end == 976702 and sgraph.strand == Strand.NEG):
found_sgraph = True
break
assert found_sgraph
# examine specific change points
trim = False
pval = 0.1
fc_cutoff = 0.8
n1 = Exon(934942, 944589)
n1_id = sgraph.get_node_id(n1)
assert sgraph.G.is_stop[n1_id]
cps = sgraph.detect_change_points(pval=pval, fc_cutoff=fc_cutoff)
for cp in cps:
sgraph.apply_change_point(cp, trim=trim)
true_starts = set([964528, 957434, 959316])
true_stops = set([944278])
assert true_starts.issubset(sgraph.start_sites)
assert true_stops.issubset(sgraph.stop_sites)
# rebuild graph and examine start/stop nodes
sgraph.recreate()
# get start/stop nodes
start_nodes, stop_nodes = sgraph.get_start_stop_nodes()
# convert to node intervals
start_nodes = set(sgraph.get_node_interval(n_id) for n_id in start_nodes)
stop_nodes = set(sgraph.get_node_interval(n_id) for n_id in stop_nodes)
assert Exon(959214, 959316) in start_nodes
assert Exon(959316, 964528) in start_nodes
assert Exon(957273, 957434) in start_nodes
assert Exon(944278, 944321) in stop_nodes
# ensure best path uses change points
pgf = PathGraphFactory(sgraph)
pgraph, k = pgf.create_optimal()
paths = find_paths(pgraph, max_paths=1)
assert len(paths) == 1
path, expr = paths[0]
path = reconstruct_path(path, pgraph, sgraph)
assert path[0] == Exon(944321, 944800)
assert path[-1] == Exon(959214, 959316)
def test_ccle55_cuff_noc2l():
'''Locus containing from 55 CCLE samples assembled with Cufflinks'''
# pull SpliceGraph out of GTF
t_dict, locus = read_single_locus('noc2l_locus.gtf')
found_sgraph = False
for sgraph in locus.create_splice_graphs():
if (sgraph.chrom == 'chr1' and sgraph.start == 934942
and sgraph.end == 976702 and sgraph.strand == Strand.NEG):
found_sgraph = True
break
assert found_sgraph
# examine specific change points
trim = False
pval = 0.1
fc_cutoff = 0.8
n1 = Exon(934942, 944589)
n1_id = sgraph.get_node_id(n1)
assert sgraph.G.is_stop[n1_id]
cps = sgraph.detect_change_points(pval=pval, fc_cutoff=fc_cutoff)
for cp in cps:
sgraph.apply_change_point(cp, trim=trim)
true_starts = set([964528, 957434, 959316])
true_stops = set([944278])
assert true_starts.issubset(sgraph.start_sites)
assert true_stops.issubset(sgraph.stop_sites)
# rebuild graph and examine start/stop nodes
sgraph.recreate()
# get start/stop nodes
start_nodes, stop_nodes = sgraph.get_start_stop_nodes()
# convert to node intervals
start_nodes = set(sgraph.get_node_interval(n_id) for n_id in start_nodes)
stop_nodes = set(sgraph.get_node_interval(n_id) for n_id in stop_nodes)
assert Exon(959214, 959316) in start_nodes
assert Exon(959316, 964528) in start_nodes
assert Exon(957273, 957434) in start_nodes
assert Exon(944278, 944321) in stop_nodes
# ensure best path uses change points
pgf = PathGraphFactory(sgraph)
pgraph, k = pgf.create_optimal()
paths = find_paths(pgraph, max_paths=1)
assert len(paths) == 1
path, expr = paths[0]
path = reconstruct_path(path, pgraph, sgraph)
assert path[0] == Exon(944321, 944800)
assert path[-1] == Exon(959214, 959316)
def assemble_isoforms(sgraph, config):
# read in transfrag paths
pgf = PathGraphFactory(sgraph)
K, k = pgf.create_optimal(kmax=config.path_graph_kmax,
loss_threshold=config.path_graph_loss_threshold,
stats_fh=config.path_graph_stats_fh)
if K is None or len(K) == 0:
return []
# smooth kmer graph
K.apply_smoothing()
genome_id_str = (
'%s:%d-%d[%s]' %
(sgraph.chrom, sgraph.start, sgraph.end, Strand.to_gtf(sgraph.strand)))
logging.debug('%s finding isoforms in k=%d graph (%d kmers) '
'source_expr=%f' %
(genome_id_str, k, len(K), K.exprs[K.SOURCE_ID]))
paths = []
for kmer_path, expr in find_paths(K, config.path_frac, config.max_paths):
path = reconstruct_path(kmer_path, K, sgraph)
paths.append((path, expr))
logging.debug('%s isoforms: %d' % (genome_id_str, len(paths)))
# build gene clusters
clusters, filtered = Cluster.build(paths, min_frac=config.isoform_frac)
logging.debug('%s gene clusters: %d filtered transfrags: %d' %
(genome_id_str, 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 assemble_isoforms(sgraph, config):
# read in transfrag paths
pgf = PathGraphFactory(sgraph)
K, k = pgf.create_optimal(kmax=config.path_graph_kmax,
stats_fh=config.path_graph_stats_fh)
if K is None or len(K) == 0:
return []
# smooth kmer graph
K.apply_smoothing()
# find isoforms
logging.debug('%s finding isoforms in k=%d graph (%d kmers) '
'source_expr=%f' % (sgraph, k, len(K), K.exprs[K.SOURCE_ID]))
paths = []
for path_kmers, expr in find_paths(K, config.path_frac, config.max_paths):
# convert path of kmers back to path of nodes in splice graph
path = K.reconstruct(path_kmers)
paths.append((path, expr))
logging.debug('%s isoforms: %d' % (sgraph, len(paths)))
# build gene clusters
clusters, filtered = Cluster.build(paths, min_frac=config.isoform_frac)
logging.debug('%s gene clusters: %d filtered transfrags: %d' %
(sgraph, len(clusters), len(filtered)))
gene_isoforms = []
for cluster in clusters:
isoforms = []
for path, expr, rel_frac, abs_frac in cluster.iterpaths():
# convert from splice graph node ids to exons
exons = sgraph.reconstruct_exons(path)
isoforms.append(
Isoform(exons=exons,
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 assemble_isoforms(sgraph, config):
# read in transfrag paths
pgf = PathGraphFactory(sgraph)
K, k = pgf.create_optimal(kmax=config.path_graph_kmax,
stats_fh=config.path_graph_stats_fh)
if K is None or len(K) == 0:
return []
# smooth kmer graph
K.apply_smoothing()
# find isoforms
logging.debug('%s finding isoforms in k=%d graph (%d kmers) '
'source_expr=%f' %
(sgraph, k, len(K), K.exprs[K.SOURCE_ID]))
paths = []
for path_kmers, expr in find_paths(K, config.path_frac, config.max_paths):
# convert path of kmers back to path of nodes in splice graph
path = K.reconstruct(path_kmers)
paths.append((path, expr))
logging.debug('%s isoforms: %d' % (sgraph, len(paths)))
# build gene clusters
clusters, filtered = Cluster.build(paths, min_frac=config.isoform_frac)
logging.debug('%s gene clusters: %d filtered transfrags: %d' %
(sgraph, len(clusters), len(filtered)))
gene_isoforms = []
for cluster in clusters:
isoforms = []
for path, expr, rel_frac, abs_frac in cluster.iterpaths():
# convert from splice graph node ids to exons
exons = sgraph.reconstruct_exons(path)
isoforms.append(Isoform(exons=exons,
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 assemble_isoforms(sgraph, config):
# read in transfrag paths
pgf = PathGraphFactory(sgraph)
K, k = pgf.create_optimal(kmax=config.path_graph_kmax,
loss_threshold=config.path_graph_loss_threshold,
stats_fh=config.path_graph_stats_fh)
if K is None or len(K) == 0:
return []
# smooth kmer graph
K.apply_smoothing()
genome_id_str = ('%s:%d-%d[%s]' %
(sgraph.chrom, sgraph.start, sgraph.end,
Strand.to_gtf(sgraph.strand)))
logging.debug('%s finding isoforms in k=%d graph (%d kmers) '
'source_expr=%f' %
(genome_id_str, k, len(K), K.exprs[K.SOURCE_ID]))
paths = []
for kmer_path, expr in find_paths(K, config.path_frac, config.max_paths):
path = reconstruct_path(kmer_path, K, sgraph)
paths.append((path, expr))
logging.debug('%s isoforms: %d' % (genome_id_str, len(paths)))
# build gene clusters
clusters, filtered = Cluster.build(paths, min_frac=config.isoform_frac)
logging.debug('%s gene clusters: %d filtered transfrags: %d' %
(genome_id_str, 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