def test_pos_neg_strand(self):
"""
positive, negative strnad
len %2 == 0 na negativnem stnadu
and not %2
"""
bam_fname = make_bam_file({
'chromosomes': [('chr1', 3000)],
'segments': [
# (qname, flag, refname, pos, mapq, cigar, tags)
('_:rbc:AAA', 16, 0, 50, 255, [(0, 100)], {
'NH': 1
}),
('_:rbc:CCC', 0, 0, 50, 255, [(0, 101)], {
'NH': 1
}),
],
})
grouped = xlsites._processs_bam_file(bam_fname, self.metrics, 10,
self.tmp)
expected = {
('chr1', '-'): {
150: {
'AAA': [(99, 50, 100, 1, 0)]
}
},
('chr1', '+'): {
49: {
'CCC': [(100, 150, 101, 1, 0)]
}
},
}
self.assertEqual(grouped, expected)
def test_run_simple(self):
bam_fname = make_bam_file(self.data)
unique_fname = get_temp_file_name(extension='.bed.gz')
multi_fname = get_temp_file_name(extension='.bed.gz')
strange_fname = get_temp_file_name(extension='.bam.gz')
result = xlsites.run(bam_fname,
unique_fname,
multi_fname,
strange_fname,
mapq_th=5,
report_progress=True)
# pylint: disable=no-member
self.assertEqual(result.all_recs, 6)
# Unmapped records:
self.assertEqual(result.notmapped_recs, 1)
# Mapped records:
self.assertEqual(result.mapped_recs, 5)
# Records with too low quality:
self.assertEqual(result.lowmapq_recs, 1)
# Records used in analysis
self.assertEqual(result.used_recs, 4)
# Records with invalid randomers
self.assertEqual(result.invalidrandomer_recs, 1)
# Records with no randomers:
self.assertEqual(result.norandomer_recs, 1)
# Barcode counter:
self.assertEqual(result.bc_cn, {'': 2, 'ACG': 1, 'CCCC': 1})
# Strange counter:
self.assertEqual(result.strange_recs, 1)
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_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_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_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_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_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_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_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_diff_barcodes(self):
"""
Different barcodes on same position.
"""
bam_fname = make_bam_file({
'chromosomes': [('chr1', 3000)],
'segments': [
# (qname, flag, refname, pos, mapq, cigar, tags)
('_:rbc:AAA', 0, 0, 50, 255, [(0, 101)], {'NH': 1}),
('_:rbc:CCC', 0, 0, 50, 255, [(0, 101)], {'NH': 1}),
('_:rbc:CCC', 0, 0, 50, 255, [(0, 101)], {'NH': 1}),
('_:rbc:GGG', 0, 0, 50, 255, [(0, 101)], {'NH': 1}),
],
}, rnd_seed=0)
grouped = list(xlsites._processs_bam_file(bam_fname, self.metrics, 10, self.tmp))
expected = [
(('chr1', '+'), 0.0167, {
49: {
'AAA': [(100, 150, 101, 1, 0)],
'CCC': [(100, 150, 101, 1, 0), (100, 150, 101, 1, 0)],
'GGG': [(100, 150, 101, 1, 0)],
}
}),
]
self.assertEqual(grouped, expected)
def setUp(self):
warnings.simplefilter("ignore", ResourceWarning)
# Temporary file names to use for output:
self.tmp1 = get_temp_file_name()
self.tmp2 = get_temp_file_name()
self.dir = get_temp_dir()
self.dir2 = get_temp_dir()
self.cross_links = make_file_from_list([
['1', '16', '17', '.', '5', '+'],
['1', '14', '15', '.', '5', '+'],
['1', '15', '16', '.', '5', '+'],
],
extension='bed')
self.peaks = make_file_from_list([
['1', '15', '16', '.', '15', '+'],
])
self.annotation = make_file_from_list([
['1', '.', 'CDS', '10', '20', '.', '+', '.', 'biotype "A";'],
['1', '.', 'ncRNA', '10', '20', '.', '+', '.', 'biotype "A";'],
['1', '.', 'CDS', '10', '20', '.', '+', '.', 'biotype "A";'],
['1', '.', 'CDS', '10', '20', '.', '+', '.', 'biotype "B";'],
['1', '.', 'CDS', '10', '20', '.', '-', '.', 'biotype "C";'],
['1', '.', 'CDS', '12', '18', '.', '+', '.', 'biotype "A";'],
['1', '.', 'CDS', '30', '40', '.', '+', '.', 'biotype "D";'],
])
self.gtf = make_file_from_list([
['1', '.', 'gene', '10', '20', '.', '+', '.', 'gene_id "A";'],
[
'1', '.', 'transcript', '10', '20', '.', '+', '.',
'gene_id "A"; transcript_id "AA";'
],
[
'1', '.', 'exon', '10', '20', '.', '+', '.',
'gene_id "A"; transcript_id "AA"; exon_number "1";'
],
])
self.bam = make_bam_file(
{
'chromosomes': [
('1', 3000),
('2', 2000),
],
'segments': [
('name3:rbc:CCCC:', 0, 0, 100, 20, [(0, 100)], {
'NH': 1
}),
('name4:ABC', 0, 0, 300, 20, [(0, 200)], {
'NH': 11
}),
]
},
rnd_seed=0)
def test_no_nh_tag(self):
data_no_nh = {
'chromosomes': [('chr1', 3000)],
'segments': [
# No NH tag is set
('name5', 0, 0, 0, 50, [(0, 100)], {})]}
bam_fname = make_bam_file(data_no_nh, rnd_seed=0)
message = r'"NH" tag not set for record: .*'
with self.assertRaisesRegex(ValueError, message):
list(xlsites._processs_bam_file(bam_fname, self.metrics, 10, self.tmp))
def test_low_quality(self):
"""
Unmapped read (FLAG=4):
"""
bam_fname = make_bam_file({
'chromosomes': [('chr1', 3000)],
'segments': [('name1', 0, 0, 0, 3, [(0, 0)], {})],
})
self.metrics.lowmapq_recs = 0
self.metrics.used_recs = 0
xlsites._processs_bam_file(bam_fname, self.metrics, 10, self.tmp)
self.assertEqual(self.metrics.lowmapq_recs, 1)
self.assertEqual(self.metrics.used_recs, 0)
def test_unmapped(self):
"""
Unmapped read (FLAG=4):
"""
bam_fname = make_bam_file({
'chromosomes': [('chr1', 3000)],
'segments': [('name1', 4, 0, 0, 0, [(0, 0)], {})],
}, rnd_seed=0)
self.metrics.all_recs = 0
self.metrics.notmapped_recs = 0
self.metrics.used_recs = 0
list(xlsites._processs_bam_file(bam_fname, self.metrics, 0, self.tmp))
self.assertEqual(self.metrics.notmapped_recs, 1)
self.assertEqual(self.metrics.all_recs, 1)
self.assertEqual(self.metrics.used_recs, 0)
