def assemble_locus(locus, transfrags, config):
# filter transfrags by expression and transfrag length
genome_id_str = '%s:%d-%d' % (locus.chrom, locus.start, locus.end)
locus_id = locus.name
num_transfrags = len(transfrags)
transfrags = filter_transfrags(transfrags,
config.min_transfrag_length,
config.min_expr,
config.transfrags_filtered_gtf_fh)
num_filtered_transfrags = len(transfrags)
logging.debug('%s locus: %s transfrags: %d filtered: %d' %
(genome_id_str, locus.name, num_transfrags,
num_filtered_transfrags))
if len(transfrags) == 0:
return
# create locus
locus = Locus.create(transfrags,
config.guided_strand,
config.guided_ends,
config.guided_assembly)
genome_id_str = '%s:%d-%d' % (locus.chrom, locus.start, locus.end)
logging.debug('%s locus: %s transfrags: %d (+: %d, -: %d, .: %d)' %
(genome_id_str, locus_id, len(transfrags),
len(locus.get_transfrags(Strand.POS)),
len(locus.get_transfrags(Strand.NEG)),
len(locus.get_transfrags(Strand.NA))))
# resolve unstranded transcripts
num_resolved = locus.impute_unknown_strands()
if num_resolved > 0:
logging.debug('%s locus: %s resolved: %d (+: %d, -: %d, .: %d)' %
(genome_id_str, locus_id, num_resolved,
len(locus.get_transfrags(Strand.POS)),
len(locus.get_transfrags(Strand.NEG)),
len(locus.get_transfrags(Strand.NA))))
# write bedgraph files after strand resolved
locus.write_bedgraph(config.bedgraph_fhs)
# write splice junctions
locus.write_splice_bed(config.splice_bed_fh)
# convert to stranded locus objects
for sgraph in locus.create_splice_graphs():
assemble_gene(sgraph, locus_id, config)
def test_create_locus():
loci = read_gtf('splice_sites.gtf')
assert len(loci) == 1
interval, gtf_lines = loci[0]
assert interval == ('chr1', 10, 525)
t_dict = Transfrag.parse_gtf(gtf_lines)
locus = Locus.create(t_dict.values())
assert locus.chrom == 'chr1'
assert locus.start == 10
assert locus.end == 525
a = locus.get_expr_data(49, 51, Strand.POS)
assert np.array_equal(a, [1.0, 2.0])
a = locus.get_expr_data(150, 151, Strand.POS)
assert np.array_equal(a, [1.0])
a = locus.get_expr_data(499, 501, Strand.POS)
assert np.array_equal(a, [3.0, 1.0])
with pytest.raises(TacoError):
locus.get_expr_data(5, 15, Strand.POS)
with pytest.raises(TacoError):
locus.get_expr_data(520, 530, Strand.POS)
def assemble_locus(locus_index, transfrags, config):
if len(transfrags) == 0:
return
# create locus
locus = Locus.create(transfrags, config.guided_strand, config.guided_ends,
config.guided_assembly)
logging.debug('%s locus: %s' % (locus, locus_index.name))
# resolve unstranded transcripts
num_resolved = locus.impute_unknown_strands()
if num_resolved > 0:
logging.debug('%s locus: %s resolved: %d' %
(locus, locus_index.name, num_resolved))
# write bedgraph files after strand resolved
locus.write_bedgraph(config.bedgraph_fhs)
# write splice junctions
locus.write_splice_bed(config.splice_bed_fh)
# convert to stranded locus objects
for sgraph in locus.create_splice_graphs():
if (sgraph.strand == Strand.NA) and not config.assemble_unstranded:
continue
assemble_gene(sgraph, locus_index.name, config)
def assemble_locus(locus, transfrags, config):
# filter transfrags by expression and transfrag length
genome_id_str = '%s:%d-%d' % (locus.chrom, locus.start, locus.end)
locus_id = locus.name
num_transfrags = len(transfrags)
transfrags = filter_transfrags(transfrags, config.min_transfrag_length,
config.min_expr,
config.transfrags_filtered_gtf_fh)
num_filtered_transfrags = len(transfrags)
logging.debug(
'%s locus: %s transfrags: %d filtered: %d' %
(genome_id_str, locus.name, num_transfrags, num_filtered_transfrags))
if len(transfrags) == 0:
return
# create locus
locus = Locus.create(transfrags, config.guided_strand, config.guided_ends,
config.guided_assembly)
genome_id_str = '%s:%d-%d' % (locus.chrom, locus.start, locus.end)
logging.debug('%s locus: %s transfrags: %d (+: %d, -: %d, .: %d)' %
(genome_id_str, locus_id, len(transfrags),
len(locus.get_transfrags(
Strand.POS)), len(locus.get_transfrags(
Strand.NEG)), len(locus.get_transfrags(Strand.NA))))
# resolve unstranded transcripts
num_resolved = locus.impute_unknown_strands()
if num_resolved > 0:
logging.debug('%s locus: %s resolved: %d (+: %d, -: %d, .: %d)' %
(genome_id_str, locus_id, num_resolved,
len(locus.get_transfrags(
Strand.POS)), len(locus.get_transfrags(Strand.NEG)),
len(locus.get_transfrags(Strand.NA))))
# write bedgraph files after strand resolved
locus.write_bedgraph(config.bedgraph_fhs)
# write splice junctions
locus.write_splice_bed(config.splice_bed_fh)
# convert to stranded locus objects
for sgraph in locus.create_splice_graphs():
assemble_gene(sgraph, locus_id, config)
def assemble_locus(locus_index, transfrags, config):
if len(transfrags) == 0:
return
# create locus
locus = Locus.create(transfrags,
config.guided_strand,
config.guided_ends,
config.guided_assembly)
logging.debug('%s locus: %s' % (locus, locus_index.name))
# resolve unstranded transcripts
num_resolved = locus.impute_unknown_strands()
if num_resolved > 0:
logging.debug('%s locus: %s resolved: %d' %
(locus, locus_index.name, num_resolved))
# write bedgraph files after strand resolved
locus.write_bedgraph(config.bedgraph_fhs)
# write splice junctions
locus.write_splice_bed(config.splice_bed_fh)
# convert to stranded locus objects
for sgraph in locus.create_splice_graphs():
if (sgraph.strand == Strand.NA) and not config.assemble_unstranded:
continue
assemble_gene(sgraph, locus_index.name, config)
def test_multi_strand1():
# read gtf and test basic values
loci = read_gtf("multi_strand1.gtf")
assert len(loci) == 1
interval, gtf_lines = loci[0]
assert interval == ("chr1", 100, 1000)
t_dict = Transfrag.parse_gtf(gtf_lines)
assert len(t_dict) == 5
locus = Locus.create(t_dict.values())
assert locus.chrom == "chr1"
assert locus.start == 100
assert locus.end == 1000
# raise exception when creating with multiple strands
with pytest.raises(TacoError):
SpliceGraph.create(t_dict.values())
transfrags_pos = locus.get_transfrags(Strand.POS)
transfrags_neg = locus.get_transfrags(Strand.NEG)
sgpos = SpliceGraph.create(transfrags_pos)
sgneg = SpliceGraph.create(transfrags_neg)
# test
assert sgpos.chrom == "chr1"
assert sgpos.start == 100
assert sgpos.end == 650
assert sgpos.strand == Strand.POS
assert sgpos.ref_start_sites == [150]
assert sgpos.ref_stop_sites == [600]
with pytest.raises(TacoError):
sgpos.get_expr_data(90, 110)
with pytest.raises(TacoError):
sgpos.get_expr_data(650, 655)
assert np.array_equal(sgpos.get_expr_data(100, 105), np.ones(5))
assert sgneg.chrom == "chr1"
assert sgneg.start == 350
assert sgneg.end == 1000
assert sgneg.strand == Strand.NEG
assert sgneg.ref_start_sites == [1000]
assert sgneg.ref_stop_sites == [350]
with pytest.raises(TacoError):
sgneg.get_expr_data(340, 350)
with pytest.raises(TacoError):
sgneg.get_expr_data(1000, 1010)
assert np.array_equal(sgneg.get_expr_data(400, 405), np.ones(5))
assert np.array_equal(sgneg.get_expr_data(945, 950), np.zeros(5))
assert np.array_equal(sgneg.get_expr_data(950, 955), np.ones(5))
assert np.array_equal(sgneg.get_expr_data(980, 985), np.zeros(5))
# test locus boundaries
bpos = tuple(sgpos._find_node_boundaries())
assert bpos == tuple((100, 200, 300, 400, 650))
bneg = tuple(sgneg._find_node_boundaries())
assert bneg == tuple((350, 400, 500, 950, 980, 1000))
# added guided ends/assembly to use boundaries from reference
lpos = SpliceGraph.create(transfrags_pos, guided_ends=True, guided_assembly=True)
bpos = tuple(lpos._find_node_boundaries())
assert bpos == tuple((100, 150, 200, 300, 400, 500, 600, 650))
lneg = SpliceGraph.create(transfrags_neg, guided_ends=True, guided_assembly=True)
bneg = tuple(lneg._find_node_boundaries())
assert bneg == tuple((350, 400, 500, 750, 900, 950, 980, 1000))
def test_multi_strand1():
# read gtf and test basic values
loci = read_gtf('multi_strand1.gtf')
assert len(loci) == 1
interval, gtf_lines = loci[0]
assert interval == ('chr1', 100, 1000)
t_dict = Transfrag.parse_gtf(gtf_lines)
assert len(t_dict) == 5
locus = Locus.create(t_dict.values())
assert locus.chrom == 'chr1'
assert locus.start == 100
assert locus.end == 1000
# raise exception when creating with multiple strands
with pytest.raises(TacoError):
SpliceGraph.create(t_dict.values())
transfrags_pos = locus.get_transfrags(Strand.POS)
transfrags_neg = locus.get_transfrags(Strand.NEG)
sgpos = SpliceGraph.create(transfrags_pos)
sgneg = SpliceGraph.create(transfrags_neg)
# test
assert sgpos.chrom == 'chr1'
assert sgpos.start == 100
assert sgpos.end == 650
assert sgpos.strand == Strand.POS
assert sgpos.ref_start_sites == [150]
assert sgpos.ref_stop_sites == [600]
with pytest.raises(TacoError):
sgpos.get_expr_data(90, 110)
with pytest.raises(TacoError):
sgpos.get_expr_data(650, 655)
assert np.array_equal(sgpos.get_expr_data(100, 105), np.ones(5))
assert sgneg.chrom == 'chr1'
assert sgneg.start == 350
assert sgneg.end == 1000
assert sgneg.strand == Strand.NEG
assert sgneg.ref_start_sites == [1000]
assert sgneg.ref_stop_sites == [350]
with pytest.raises(TacoError):
sgneg.get_expr_data(340, 350)
with pytest.raises(TacoError):
sgneg.get_expr_data(1000, 1010)
assert np.array_equal(sgneg.get_expr_data(400, 405), np.ones(5))
assert np.array_equal(sgneg.get_expr_data(945, 950), np.zeros(5))
assert np.array_equal(sgneg.get_expr_data(950, 955), np.ones(5))
assert np.array_equal(sgneg.get_expr_data(980, 985), np.zeros(5))
# test locus boundaries
bpos = tuple(sgpos._find_node_boundaries())
assert bpos == tuple((100, 200, 300, 400, 650))
bneg = tuple(sgneg._find_node_boundaries())
assert bneg == tuple((350, 400, 500, 950, 980, 1000))
# added guided ends/assembly to use boundaries from reference
lpos = SpliceGraph.create(transfrags_pos,
guided_ends=True,
guided_assembly=True)
bpos = tuple(lpos._find_node_boundaries())
assert bpos == tuple((100, 150, 200, 300, 400, 500, 600, 650))
lneg = SpliceGraph.create(transfrags_neg,
guided_ends=True,
guided_assembly=True)
bneg = tuple(lneg._find_node_boundaries())
assert bneg == tuple((350, 400, 500, 750, 900, 950, 980, 1000))