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_gene(
locus_chrom,
locus_id_str,
gene_id_value_obj,
tss_id_value_obj,
t_id_value_obj,
G,
strand,
partial_paths,
config,
gtf_fileh,
bed_fileh,
):
# run assembly algorithm
path_info_list = assemble_transcript_graph(
G, strand, partial_paths, config.kmax, config.ksensitivity, config.fraction_major_isoform, config.max_paths
)
logging.debug("\tAssembled %d transcript(s)" % (len(path_info_list)))
# determine gene ids and tss ids
annotate_gene_and_tss_ids(path_info_list, strand, gene_id_value_obj, tss_id_value_obj)
# bin transcripts by gene id
gene_path_info_dict = collections.defaultdict(lambda: [])
for p in path_info_list:
gene_path_info_dict[p.gene_id].append(p)
for gene_path_info_list in gene_path_info_dict.itervalues():
# highest scoring path is always first in list
highest_score = max(1e-8, gene_path_info_list[0].score)
# create GTF features for each transcript path
for p in gene_path_info_list:
# assign transcript id
t_id = t_id_value_obj.next()
# get strings for each id
t_id_str = "TU%d" % t_id
tss_id_str = "TSS%d" % (p.tss_id)
gene_id_str = "G%d" % (p.gene_id)
# compute isoform fractions
frac = p.score / highest_score
# write to GTF
if config.create_gtf:
for f in get_gtf_features(
locus_chrom,
strand,
p.path,
locus_id=locus_id_str,
gene_id=gene_id_str,
tss_id=tss_id_str,
transcript_id=t_id_str,
score=p.score,
frac=frac,
):
print >> gtf_fileh, str(f)
# write to BED
if config.create_bed:
name = "%s|%s(%.1f)" % (gene_id_str, t_id_str, p.score)
fields = write_bed(locus_chrom, name, strand, int(round(1000.0 * frac)), p.path)
print >> bed_fileh, "\t".join(fields)
def assemble_gene(locus_chrom, locus_id_str,
gene_id_value_obj, tss_id_value_obj, t_id_value_obj,
G, strand, partial_paths,
config, gtf_fileh, bed_fileh):
# run assembly algorithm
path_info_list = assemble_transcript_graph(G, strand, partial_paths,
config.kmax,
config.ksensitivity,
config.fraction_major_isoform,
config.max_paths)
logging.debug("\tAssembled %d transcript(s)" % (len(path_info_list)))
# determine gene ids and tss ids
annotate_gene_and_tss_ids(path_info_list, strand,
gene_id_value_obj,
tss_id_value_obj)
# bin transcripts by gene id
gene_path_info_dict = collections.defaultdict(lambda: [])
for p in path_info_list:
gene_path_info_dict[p.gene_id].append(p)
for gene_path_info_list in gene_path_info_dict.itervalues():
# highest scoring path is always first in list
highest_score = max(1e-8, gene_path_info_list[0].score)
# create GTF features for each transcript path
for p in gene_path_info_list:
# assign transcript id
t_id = t_id_value_obj.next()
# get strings for each id
t_id_str = "TU%d" % t_id
tss_id_str = "TSS%d" % (p.tss_id)
gene_id_str = "G%d" % (p.gene_id)
# compute isoform fractions
frac = p.score / highest_score
# write to GTF
if config.create_gtf:
for f in get_gtf_features(locus_chrom, strand, p.path,
locus_id=locus_id_str,
gene_id=gene_id_str,
tss_id=tss_id_str,
transcript_id=t_id_str,
score=p.score,
frac=frac):
print >>gtf_fileh, str(f)
# write to BED
if config.create_bed:
name = "%s|%s(%.1f)" % (gene_id_str, t_id_str, p.score)
fields = write_bed(locus_chrom, name, strand,
int(round(1000.0*frac)), p.path)
print >>bed_fileh, '\t'.join(fields)
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 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")
tdict = dict((t.attrs['transcript_id'],t) for t in transcripts)
# set transcript scores
tdict["ABCDE"].score = 2.0
tdict["ACE"].score = 1.0
tdict["ABCE"].score = 1.0
tdict["ACDE"].score = 1.0
# create graphs
GS = create_transcript_graphs('chr1', transcripts,
create_bedgraph=False,
bedgraph_filehs=None,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.0)
Gsub, strand, partial_paths = GS[0].Gsub, GS[0].strand, GS[0].partial_paths
# assemble with kmax=2
results = list(assemble_transcript_graph(Gsub, strand, partial_paths,
user_kmax=2,
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)
# change transcript scores
tdict["ABCDE"].score = 4.0
tdict["ACE"].score = 3.0
tdict["ABCE"].score = 2.0
tdict["ACDE"].score = 1.0
# create graphs
GS = create_transcript_graphs('chr1', transcripts,
create_bedgraph=False,
bedgraph_filehs=None,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.0)
Gsub, strand, partial_paths = GS[0].Gsub, GS[0].strand, GS[0].partial_paths
# assemble with kmax=3
results = list(assemble_transcript_graph(Gsub, strand, partial_paths,
user_kmax=3,
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)
return
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")
tdict = dict((t.attrs['transcript_id'], t) for t in transcripts)
# set transcript scores
tdict["ABCDE"].score = 2.0
tdict["ACE"].score = 1.0
tdict["ABCE"].score = 1.0
tdict["ACDE"].score = 1.0
# create graphs
GS = create_transcript_graphs('chr1',
transcripts,
create_bedgraph=False,
bedgraph_filehs=None,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.0)
Gsub, strand, partial_paths = GS[0].Gsub, GS[0].strand, GS[
0].partial_paths
# assemble with kmax=2
results = list(
assemble_transcript_graph(Gsub,
strand,
partial_paths,
user_kmax=2,
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)
# change transcript scores
tdict["ABCDE"].score = 4.0
tdict["ACE"].score = 3.0
tdict["ABCE"].score = 2.0
tdict["ACDE"].score = 1.0
# create graphs
GS = create_transcript_graphs('chr1',
transcripts,
create_bedgraph=False,
bedgraph_filehs=None,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.0)
Gsub, strand, partial_paths = GS[0].Gsub, GS[0].strand, GS[
0].partial_paths
# assemble with kmax=3
results = list(
assemble_transcript_graph(Gsub,
strand,
partial_paths,
user_kmax=3,
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)
return
