def test_negative_strand(self):
"""
Whole read is in single transcript, single segment. But the segment
borders on intergenic (downstream).
"""
gtf_neg_data = [
i[:6] + ['-'] + i[7:] for i in intervals_to_list(self.gtf_data)
]
gtf_neg = make_file_from_list(gtf_neg_data)
bam = make_bam_file({
'chromosomes': [('1', 1000)],
'segments': [
# (qname, flag, refname, pos, mapq, cigar, tags)
('name2:rbc:CCCC', 16, 0, 549, 255, [(0, 30)], {
'NH': 1
}),
]
})
expected = [
['RNAmap', 'type', 'position', 'all', 'explicit'],
['CDS-intergenic', '20', '0.5', '0'],
['intergenic-CDS', '-80', '0.5', '0'],
]
rnamaps.run(bam,
gtf_neg,
self.out,
self.strange,
self.cross_tr,
mismatches=1,
implicit_handling='split')
self.assertEqual(expected, make_list_from_file(self.out))
def test_explicit_whole_in(self):
"""
Whole read is in single transcript and is crossing the exon-intron
landmark (it is explicit). Provide three reads, with two different
cross-links. One cross-link has two distinct randomers.
"""
bam = make_bam_file({
'chromosomes': [('1', 1000)],
'segments': [
# (qname, flag, refname, pos, mapq, cigar, tags)
('name2:rbc:CCCC', 0, 0, 140, 255, [(0, 50)], {
'NH': 1
}),
('name2:rbc:AAAA', 0, 0, 142, 255, [(0, 50)], {
'NH': 1
}),
('name2:rbc:CCCC', 0, 0, 142, 255, [(0, 50)], {
'NH': 1
}),
]
})
expected = [
['RNAmap', 'type', 'position', 'all', 'explicit'],
['UTR5-intron', '-10', '1', '1'],
['UTR5-intron', '-8', '2', '2'],
]
rnamaps.run(bam,
self.gtf,
self.out,
self.strange,
self.cross_tr,
mismatches=1)
self.assertEqual(expected, make_list_from_file(self.out))
def test_implicit_exons(self):
"""
Whole read is in single transcript and in single segment. Also, this
segment is of EXON_TYPE in the "middle" segment in transcript. Only one read.
"""
bam = make_bam_file({
'chromosomes': [('1', 1000)],
'segments': [
# (qname, flag, refname, pos, mapq, cigar, tags)
('name2:rbc:CCCC', 0, 0, 205, 255, [(0, 20)], {
'NH': 1
}),
]
})
expected = [
['RNAmap', 'type', 'position', 'all', 'explicit'],
['CDS-UTR3', '-25', '0.25', '0'],
['CDS-intron', '-25', '0.25', '0'],
['UTR5-CDS', '5', '0.25', '0'],
['intron-CDS', '5', '0.25', '0'],
]
rnamaps.run(bam,
self.gtf,
self.out,
self.strange,
self.cross_tr,
mismatches=1,
implicit_handling='split')
self.assertEqual(expected, make_list_from_file(self.out))
def test_implicit_intergenic(self):
"""
Whole read is in intergenic.
"""
bam = make_bam_file({
'chromosomes': [('1', 1000)],
'segments': [
# (qname, flag, refname, pos, mapq, cigar, tags)
('name2:rbc:CCCC', 0, 0, 530, 255, [(0, 30)], {
'NH': 1
}),
]
})
expected = [
['RNAmap', 'type', 'position', 'all', 'explicit'],
['CDS-intergenic', '30', '0.5', '0'],
['intergenic-CDS', '-70', '0.5', '0'],
]
rnamaps.run(bam,
self.gtf,
self.out,
self.strange,
self.cross_tr,
mismatches=1,
implicit_handling='split')
self.assertEqual(expected, make_list_from_file(self.out))
def test_implicit_whole_in(self):
"""
Whole read is in single transcript and in single segment. Also, this
segment is the "middle" segment in transcript. Provide three reads, with
two different cross-links. One cross-link has two distinct randomers.
"""
bam = make_bam_file({
'chromosomes': [('1', 1000)],
'segments': [
# (qname, flag, refname, pos, mapq, cigar, tags)
('name2:rbc:CCCC', 0, 0, 160, 255, [(0, 30)], {
'NH': 1
}),
('name2:rbc:CCCC', 0, 0, 163, 255, [(0, 30)], {
'NH': 1
}),
('name2:rbc:GGGG', 0, 0, 163, 255, [(0, 30)], {
'NH': 1
}),
]
})
expected = [
['RNAmap', 'type', 'position', 'all', 'explicit'],
['UTR5-intron', '10', '1', '0'],
['UTR5-intron', '13', '2', '0'],
]
rnamaps.run(bam,
self.gtf,
self.out,
self.strange,
self.cross_tr,
mismatches=1)
self.assertEqual(expected, make_list_from_file(self.out))
def test_cross_transcript_read(self):
"""
Read is half in transcript region and half in intergenic.
"""
bam = make_bam_file({
'chromosomes': [('1', 1000)],
'segments': [
# (qname, flag, refname, pos, mapq, cigar, tags)
('name2:rbc:CCCC', 0, 0, 235, 255, [(0, 50)], {
'NH': 1
}),
]
})
expected = [
[
'chrom', 'strand', 'xlink', 'second-start', 'end-position',
'read_len'
],
['1', '+', '234', '0', '284', '50'],
]
rnamaps.run(bam,
self.gtf,
self.out,
self.strange,
self.cross_tr,
mismatches=1)
self.assertEqual(expected, make_list_from_file(self.cross_tr))
def test_explicit_intergenic_right(self):
"""
Read is half in transcript region and half in intergenic.
"""
bam = make_bam_file({
'chromosomes': [('1', 1000)],
'segments': [
# (qname, flag, refname, pos, mapq, cigar, tags)
('name2:rbc:CCCC', 0, 0, 480, 255, [(0, 50)], {
'NH': 1
}),
]
})
expected = [
['RNAmap', 'type', 'position', 'all', 'explicit'],
['CDS-intergenic', '-20', '1', '1'],
]
rnamaps.run(bam,
self.gtf,
self.out,
self.strange,
self.cross_tr,
mismatches=1)
self.assertEqual(expected, make_list_from_file(self.out))
def test_implicit_inter_tr(self):
"""
Whole read is in single transcript, single segment. But the segment
borders on intergenic (downstream).
"""
bam = make_bam_file(
{
'chromosomes': [('1', 1000)],
'segments': [
# (qname, flag, refname, pos, mapq, cigar, tags)
('name2:rbc:CCCC', 0, 0, 610, 255, [(0, 30)], {
'NH': 1
}),
]
},
rnd_seed=0)
expected = [
['RNAmap', 'type', 'position', 'all', 'explicit'],
['CDS-CDS', '-40', '0.3333', '0'],
['CDS-intron', '-40', '0.3333', '0'],
['intergenic-CDS', '10', '0.3333', '0'],
]
rnamaps.run(bam,
self.gtf,
self.out,
self.strange,
self.cross_tr,
mismatches=1,
implicit_handling='split')
self.assertEqual(expected, make_list_from_file(self.out))
def test_run(self):
landmarks = make_file_from_list(
sort=True,
data=[
['chr1', '210', '211', 'gene-start;A', '.', '+'],
['chr1', '270', '271', 'translation-start;A', '.', '+'],
['chr1', '299', '300', 'noncoding-gene-end;B', '.', '-'],
['chr1', '330', '331', 'exon-intron;A', '.', '+'],
['chr1', '490', '491', 'intron-exon;A', '.', '+'],
['chr1', '550', '551', 'translation-end;A', '.', '+'],
['chr1', '749', '750', 'noncoding-gene-start;B', '.', '-'],
['chr1', '760', '761', 'gene-end;A', '.', '+'],
])
sites = make_file_from_list([
['chr1', '220', '221', '.', '1', '+'],
['chr1', '350', '351', '.', '1', '+'],
['chr1', '350', '351', '.', '1', '-'],
['chr1', '550', '551', '.', '1', '+'],
['chr1', '740', '741', '.', '1', '+'],
['chr1', '750', '751', '.', '1', '-'],
])
rnamaps.run(sites, landmarks, outdir=self.outdir)
self.assertTrue(os.path.isdir(self.outdir))
sites_name = remove_extension(sites, ['.bed', '.bed.gz'])
for maptype in rnamaps.RNAMAP_TYPES:
basename = os.path.join(self.outdir,
'{}_{}'.format(sites_name, maptype))
# for extension in ['.tsv', '.png', '_plot_data.txt']:
for extension in ['.tsv', '.png']:
fname = basename + extension
self.assertTrue(os.path.isfile(fname))
self.assertGreater(os.path.getsize(fname), 1)
def test_run(self):
regions = make_file_from_list(
sort=True,
data=[
[
'chr1', '.', 'intergenic', '1', '210', '.', '+', '.',
'gene_name "None";'
],
[
'chr1', '.', 'UTR5', '211', '270', '.', '+', '.',
'gene_name "A";'
],
[
'chr1', '.', 'CDS', '271', '330', '.', '+', '.',
'gene_name "A";'
],
[
'chr1', '.', 'intron', '331', '490', '.', '+', '.',
'gene_name "A";'
],
[
'chr1', '.', 'CDS', '491', '550', '.', '+', '.',
'gene_name "A";'
],
[
'chr1', '.', 'UTR3', '551', '760', '.', '+', '.',
'gene_name "A";'
],
[
'chr1', '.', 'intergenic', '761', '1100', '.', '+', '.',
'gene_name "None";'
],
[
'chr1', '.', 'intergenic', '1', '300', '.', '-', '.',
'gene_name "None";'
],
[
'chr1', '.', 'ncRNA', '301', '500', '.', '-', '.',
'gene_name "B";'
],
[
'chr1', '.', 'intron', '501', '600', '.', '-', '.',
'gene_name "B";'
],
[
'chr1', '.', 'ncRNA', '601', '750', '.', '-', '.',
'gene_name "B";'
],
[
'chr1', '.', 'intergenic', '751', '1000', '.', '-', '.',
'gene_name "None";'
],
])
sites = make_file_from_list([
['chr1', '220', '221', '.', '1', '+'],
['chr1', '350', '351', '.', '1', '+'],
['chr1', '350', '351', '.', '1', '-'],
['chr1', '550', '551', '.', '1', '+'],
['chr1', '740', '741', '.', '1', '+'],
['chr1', '750', '751', '.', '1', '-'],
])
rnamaps.run(sites, regions, outdir=self.outdir)
self.assertTrue(os.path.isdir(self.outdir))
sites_name = remove_extension(sites, ['.bed', '.bed.gz'])
for maptype in rnamaps.MAP_TYPES:
basename = os.path.join(self.outdir,
'{}_{}'.format(sites_name, maptype))
# for extension in ['.tsv', '.png', '_plot_data.txt']:
for extension in ['.tsv', '.png']:
fname = basename + extension
self.assertTrue(os.path.isfile(fname))
self.assertGreater(os.path.getsize(fname), 1)
