def test_run_keep_unmapped_with_quals(self):
'''test run keep unmapped bam has quality scores'''
outprefix = 'tmp.bamfilter_run'
b = bamfilter.BamFilter(
os.path.join(data_dir, 'bamfilter_test_run_with_qual.bam'),
outprefix,
fastq_out=False,
length_cutoff=600,
min_read_length=100,
contigs_to_use={'contig1', 'contig3', 'contig4'}
)
b.run()
expected = os.path.join(data_dir, 'bamfilter_test_run_keep_unmapped.out.reads.fa')
self.assertTrue(filecmp.cmp(expected, outprefix + '.fasta', shallow=False))
os.unlink(outprefix + '.fasta')
os.unlink(outprefix + '.log')
b = bamfilter.BamFilter(
os.path.join(data_dir, 'bamfilter_test_run_with_qual.bam'),
outprefix,
fastq_out=True,
length_cutoff=600,
min_read_length=100,
contigs_to_use={'contig1', 'contig3', 'contig4'}
)
b.run()
expected = os.path.join(data_dir, 'bamfilter_test_run_keep_unmapped.out.reads.fq')
self.assertTrue(filecmp.cmp(expected, outprefix + '.fastq', shallow=False))
os.unlink(outprefix + '.fastq')
os.unlink(outprefix + '.log')
def test_check_contigs_to_use(self):
'''test _check_contigs_to_use'''
input_bam = os.path.join(data_dir, 'bamfilter_test_check_contigs_to_use.bam')
b = bamfilter.BamFilter(input_bam, 'out')
ref_lengths = b._get_ref_lengths()
self.assertTrue(b._check_contigs_to_use(ref_lengths))
b = bamfilter.BamFilter(input_bam, 'out', contigs_to_use={'1'})
self.assertTrue(b._check_contigs_to_use(ref_lengths))
b = bamfilter.BamFilter(input_bam, 'out', contigs_to_use={'1', '2'})
self.assertTrue(b._check_contigs_to_use(ref_lengths))
with self.assertRaises(bamfilter.Error):
b = bamfilter.BamFilter(input_bam, 'out', contigs_to_use={'42'})
self.assertTrue(b._check_contigs_to_use(ref_lengths))
def test_get_contigs_to_use(self):
'''test _get_contigs_to_use'''
b = bamfilter.BamFilter(os.path.join(data_dir, 'bamfilter_test_get_contigs_to_use.bam'), 'out')
test_file = os.path.join(data_dir, 'bamfilter_test_get_contigs_to_use.infile')
self.assertEqual(b._get_contigs_to_use(test_file), {'contig42', 'contig4444244'})
self.assertEqual(b._get_contigs_to_use(None), set())
self.assertEqual(b._get_contigs_to_use({'42', '43'}), {'42', '43'})
def test_get_ref_lengths(self):
'''test _get_ref_lengths'''
b = bamfilter.BamFilter(os.path.join(data_dir, 'bamfilter_test_get_ref_lengths.bam'), 'out')
expected = {
'ref1': 41,
'ref2': 42,
'ref3': 43,
}
self.assertEqual(expected, b._get_ref_lengths())
def test_get_region_start(self):
'''test _get_region start'''
b = bamfilter.BamFilter(os.path.join(data_dir, 'bamfilter_test_get_region_start.bam'), 'out')
expected = os.path.join(data_dir, 'bamfilter_test_get_region_start.reads.fa')
tmp = 'tmp.test_get_region.out.fa'
f = pyfastaq.utils.open_file_write(tmp)
b._get_region('1', 0, 64, f, min_length=20)
pyfastaq.utils.close(f)
self.assertTrue(filecmp.cmp(expected, tmp, shallow=False))
os.unlink(tmp)
def test_exclude_region(self):
'''test _exclude_region'''
b = bamfilter.BamFilter(os.path.join(data_dir, 'bamfilter_test_exclude_region.bam'), 'out')
expected = os.path.join(data_dir, 'bamfilter_test_exclude_region.reads.fa')
tmp = 'tmp.test_exclude_reads.out.fa'
f = pyfastaq.utils.open_file_write(tmp)
b._exclude_region('1', 500, 700, f)
pyfastaq.utils.close(f)
self.assertTrue(filecmp.cmp(expected, tmp, shallow=False))
os.unlink(tmp)
def test_break_reads(self):
'''test _break_reads'''
b = bamfilter.BamFilter(os.path.join(data_dir, 'bamfilter_test_break_reads.bam'), 'out')
expected = os.path.join(data_dir, 'bamfilter_test_break_reads.broken_reads.fa')
tmp = 'tmp.test_break_reads.out.fa'
f = pyfastaq.utils.open_file_write(tmp)
b._break_reads('contig1', 390, f, min_read_length=5)
pyfastaq.utils.close(f)
self.assertTrue(filecmp.cmp(expected, tmp, shallow=False))
os.unlink(tmp)
def test_get_all_unmapped_reads(self):
'''test _get_all_unmapped_reads'''
b = bamfilter.BamFilter(os.path.join(data_dir, 'bamfilter_test_get_all_unmapped_reads.bam'), 'out')
expected = os.path.join(data_dir, 'bamfilter_test_get_all_unmapped_reads.reads.fa')
tmp = 'tmp.test_get_all_unmapped_reads.out.fa'
f = pyfastaq.utils.open_file_write(tmp)
b._get_all_unmapped_reads(f)
pyfastaq.utils.close(f)
self.assertTrue(filecmp.cmp(expected, tmp, shallow=False))
os.unlink(tmp)
def test_all_reads_from_contig(self):
'''test _all_reads_from_contig'''
b = bamfilter.BamFilter(os.path.join(data_dir, 'bamfilter_test_all_reads_from_contig.bam'), 'out')
tmp = 'tmp.test_all_reads_from_contig.out.fa'
f = pyfastaq.utils.open_file_write(tmp)
expected = os.path.join(data_dir, 'bamfilter_test_all_reads_from_contig.reads.fa')
b._all_reads_from_contig('1', f)
pyfastaq.utils.close(f)
self.assertTrue(filecmp.cmp(expected, tmp, shallow=False))
os.unlink(tmp)
def test_run_discard_unmapped(self):
'''test run keep unmapped'''
outprefix = 'tmp.bamfilter_run'
b = bamfilter.BamFilter(
os.path.join(data_dir, 'bamfilter_test_run.bam'),
outprefix,
length_cutoff=600,
min_read_length=100,
contigs_to_use={'contig1', 'contig3', 'contig4'},
discard_unmapped=True)
b.run()
expected = os.path.join(
data_dir, 'bamfilter_test_run_discard_unmapped.out.reads.fa')
self.assertTrue(
filecmp.cmp(expected, outprefix + '.fasta', shallow=False))
os.unlink(outprefix + '.fasta')
os.unlink(outprefix + '.log')