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 = 0.05
fc_cutoff = 0.8
n1 = Exon(934942, 944589)
n1_id = sgraph.get_node_id(n1)
assert sgraph.G.node[n1_id][SGNode.IS_STOP]
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
config = Config.defaults()
config.max_paths = 1
gene_isoforms = assemble_isoforms(sgraph, config)
assert len(gene_isoforms) == 1
isoforms = gene_isoforms[0]
assert len(isoforms) == 1
isoform = isoforms[0]
assert isoform.path[0] == Exon(944321, 944800)
assert isoform.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
config = Config.defaults()
config.max_paths = 1
gene_isoforms = assemble_isoforms(sgraph, config)
assert len(gene_isoforms) == 1
isoforms = gene_isoforms[0]
assert len(isoforms) == 1
isoform = isoforms[0]
assert isoform.path[0] == Exon(944321, 944800)
assert isoform.path[-1] == Exon(959214, 959316)
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)
isoforms = assemble_isoforms(sgraph, Config.defaults())
assert len(isoforms) == 0
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)
isoforms = assemble_isoforms(sgraph, Config.defaults())
assert len(isoforms) == 0
