def test_assembler1(self):
# setup correct transcripts
PATH_ABCDE = tuple([Exon(0,100), Exon(200,300), Exon(400,500),Exon(600,700), Exon(800,900)])
PATH_ACE = tuple([Exon(0,100), Exon(400,500), Exon(800,900)])
PATH_ABCE = tuple([Exon(0,100), Exon(200,300), Exon(400,500), Exon(800,900)])
PATH_ACDE = tuple([Exon(0,100), Exon(400,500),Exon(600,700), Exon(800,900)])
# read transcripts
transcripts = read_first_locus("assemble1.gtf", score_attr="score")
GG = get_transcript_graphs(transcripts)
G,tmap = GG[POS_STRAND]
# set transcript scores
tmap["ABCDE"].score = 2.0
tmap["ACE"].score = 1.0
tmap["ABCE"].score = 1.0
tmap["ACDE"].score = 1.0
# set assembly parameter
kmax = 2
# assemble
GS = list(prune_transcript_graph(G, POS_STRAND, tmap,
min_trim_length=0,
trim_utr_fraction=0,
trim_intron_fraction=0))
Gsub, strand, partial_paths = GS[0]
results = list(assemble_transcript_graph(Gsub, strand, partial_paths,
user_kmax=kmax,
ksensitivity=0,
fraction_major_path=0,
max_paths=1000))
self.assertEquals(len(results), 2)
self.assertEqual(tuple(results[0].path), PATH_ABCDE)
self.assertAlmostEqual(results[0].score, 3.0, places=3)
self.assertEqual(tuple(results[1].path), PATH_ACE)
self.assertAlmostEqual(results[1].score, 2.0, places=3)
# set transcript scores
tmap["ABCDE"].score = 4.0
tmap["ACE"].score = 3.0
tmap["ABCE"].score = 2.0
tmap["ACDE"].score = 1.0
# set assembly parameter
kmax = 3
# assemble
GS = list(prune_transcript_graph(G, POS_STRAND, tmap,
min_trim_length=0,
trim_utr_fraction=0,
trim_intron_fraction=0))
Gsub, strand, partial_paths = GS[0]
results = list(assemble_transcript_graph(Gsub, strand, partial_paths,
user_kmax=kmax,
ksensitivity=0,
fraction_major_path=0,
max_paths=1000))
self.assertEquals(len(results), 4)
self.assertEqual(tuple(results[0].path), PATH_ABCDE)
self.assertAlmostEqual(results[0].score, 4.0, places=3)
self.assertEqual(tuple(results[1].path), PATH_ACE)
self.assertAlmostEqual(results[1].score, 3.0, places=3)
self.assertEqual(tuple(results[2].path), PATH_ABCE)
self.assertAlmostEqual(results[2].score, 2.0, places=3)
self.assertEqual(tuple(results[3].path), PATH_ACDE)
self.assertAlmostEqual(results[3].score, 1.0, places=3)
def assemble_locus(
transcripts,
locus_id_value_obj,
gene_id_value_obj,
tss_id_value_obj,
t_id_value_obj,
config,
gtf_fileh,
bed_fileh,
bedgraph_filehs,
):
def get_bedgraph_lines(chrom, G):
for n in sorted(G.nodes()):
if n.start < 0:
continue
fields = (chrom, n.start, n.end, G.node[n][NODE_SCORE])
yield fields
# gather properties of locus
locus_chrom = transcripts[0].chrom
locus_start = transcripts[0].start
locus_end = max(tx.end for tx in transcripts)
logging.debug("[LOCUS] %s:%d-%d %d transcripts" % (locus_chrom, locus_start, locus_end, len(transcripts)))
locus_id_str = "L%d" % (locus_id_value_obj.next())
# filter transcripts
logging.debug("\tFiltering transcripts")
transcripts = filter_transcripts(transcripts, config.min_transcript_length, config.guided)
# build transcript graphs
for G, strand, strand_transcripts in create_transcript_graphs(transcripts):
# output bedgraph
if config.create_bedgraph:
for fields in get_bedgraph_lines(locus_chrom, G):
print >>bedgraph_filehs[strand], "\t".join(map(str, fields))
# process transcript graphs
for Gsub, strand, partial_paths in prune_transcript_graph(
G, strand, strand_transcripts, config.min_trim_length, config.trim_utr_fraction, config.trim_intron_fraction
):
logging.debug(
"Subgraph %s:%d-%d(%s) %d nodes %d paths"
% (locus_chrom, locus_start, locus_end, strand_int_to_str(strand), len(Gsub), len(partial_paths))
)
# assemble subgraph
assemble_gene(
locus_chrom,
locus_id_str,
gene_id_value_obj,
tss_id_value_obj,
t_id_value_obj,
Gsub,
strand,
partial_paths,
config,
gtf_fileh,
bed_fileh,
)
def assemble_locus(transcripts,
locus_id_value_obj,
gene_id_value_obj,
tss_id_value_obj,
t_id_value_obj,
config,
gtf_fileh,
bed_fileh,
bedgraph_filehs):
def get_bedgraph_lines(chrom, G):
for n in sorted(G.nodes()):
if n.start < 0:
continue
fields = (chrom, n.start, n.end, G.node[n][NODE_SCORE])
yield fields
# gather properties of locus
locus_chrom = transcripts[0].chrom
locus_start = transcripts[0].start
locus_end = max(tx.end for tx in transcripts)
logging.debug("[LOCUS] %s:%d-%d %d transcripts" %
(locus_chrom, locus_start, locus_end,
len(transcripts)))
locus_id_str = "L%d" % (locus_id_value_obj.next())
# filter transcripts
logging.debug("\tFiltering transcripts")
transcripts = filter_transcripts(transcripts,
config.min_transcript_length,
config.guided)
# build transcript graphs
for G, strand, strand_transcripts in \
create_transcript_graphs(transcripts):
# output bedgraph
if config.create_bedgraph:
for fields in get_bedgraph_lines(locus_chrom, G):
print >>bedgraph_filehs[strand], '\t'.join(map(str,fields))
# process transcript graphs
for Gsub, strand, partial_paths in \
prune_transcript_graph(G, strand, strand_transcripts,
config.min_trim_length,
config.trim_utr_fraction,
config.trim_intron_fraction):
logging.debug("Subgraph %s:%d-%d(%s) %d nodes %d paths" %
(locus_chrom, locus_start, locus_end,
strand_int_to_str(strand), len(Gsub),
len(partial_paths)))
# assemble subgraph
assemble_gene(locus_chrom, locus_id_str,
gene_id_value_obj,
tss_id_value_obj,
t_id_value_obj,
Gsub, strand, partial_paths,
config,
gtf_fileh,
bed_fileh)
def test_assembler1(self):
# setup correct transcripts
PATH_ABCDE = tuple([
Exon(0, 100),
Exon(200, 300),
Exon(400, 500),
Exon(600, 700),
Exon(800, 900)
])
PATH_ACE = tuple([Exon(0, 100), Exon(400, 500), Exon(800, 900)])
PATH_ABCE = tuple(
[Exon(0, 100),
Exon(200, 300),
Exon(400, 500),
Exon(800, 900)])
PATH_ACDE = tuple(
[Exon(0, 100),
Exon(400, 500),
Exon(600, 700),
Exon(800, 900)])
# read transcripts
transcripts = read_first_locus("assemble1.gtf", score_attr="score")
GG = get_transcript_graphs(transcripts)
G, tmap = GG[POS_STRAND]
# set transcript scores
tmap["ABCDE"].score = 2.0
tmap["ACE"].score = 1.0
tmap["ABCE"].score = 1.0
tmap["ACDE"].score = 1.0
# set assembly parameter
kmax = 2
# assemble
GS = list(
prune_transcript_graph(G,
POS_STRAND,
tmap,
min_trim_length=0,
trim_utr_fraction=0,
trim_intron_fraction=0))
Gsub, strand, partial_paths = GS[0]
results = list(
assemble_transcript_graph(Gsub,
strand,
partial_paths,
user_kmax=kmax,
ksensitivity=0,
fraction_major_path=0,
max_paths=1000))
self.assertEquals(len(results), 2)
self.assertEqual(tuple(results[0].path), PATH_ABCDE)
self.assertAlmostEqual(results[0].score, 3.0, places=3)
self.assertEqual(tuple(results[1].path), PATH_ACE)
self.assertAlmostEqual(results[1].score, 2.0, places=3)
# set transcript scores
tmap["ABCDE"].score = 4.0
tmap["ACE"].score = 3.0
tmap["ABCE"].score = 2.0
tmap["ACDE"].score = 1.0
# set assembly parameter
kmax = 3
# assemble
GS = list(
prune_transcript_graph(G,
POS_STRAND,
tmap,
min_trim_length=0,
trim_utr_fraction=0,
trim_intron_fraction=0))
Gsub, strand, partial_paths = GS[0]
results = list(
assemble_transcript_graph(Gsub,
strand,
partial_paths,
user_kmax=kmax,
ksensitivity=0,
fraction_major_path=0,
max_paths=1000))
self.assertEquals(len(results), 4)
self.assertEqual(tuple(results[0].path), PATH_ABCDE)
self.assertAlmostEqual(results[0].score, 4.0, places=3)
self.assertEqual(tuple(results[1].path), PATH_ACE)
self.assertAlmostEqual(results[1].score, 3.0, places=3)
self.assertEqual(tuple(results[2].path), PATH_ABCE)
self.assertAlmostEqual(results[2].score, 2.0, places=3)
self.assertEqual(tuple(results[3].path), PATH_ACDE)
self.assertAlmostEqual(results[3].score, 1.0, places=3)
