def test_bmtagger_empty_input(self):
empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
out_bam = util.file.mkstempfname('-out.bam')
args = taxon_filter.parser_deplete_bam_bmtagger(argparse.ArgumentParser()).parse_args([
empty_bam, self.database_prefix_path, out_bam, '--srprismMemory', '1500'])
args.func_main(args)
assert_equal_bam_reads(self, out_bam, empty_bam)
def test_bmtagger_empty_input(self):
empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
out_bam = util.file.mkstempfname('-out.bam')
args = taxon_filter.parser_deplete_bam_bmtagger(
argparse.ArgumentParser()).parse_args(
[empty_bam, self.database_prefix_path, out_bam])
args.func_main(args)
assert_equal_bam_reads(self, out_bam, empty_bam)
def test_deplete_bmtagger_bam(self):
inBam = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam')
outBam = util.file.mkstempfname('-out.bam')
args = taxon_filter.parser_deplete_bam_bmtagger(argparse.ArgumentParser()).parse_args([
inBam, self.database_prefix_path, outBam, '--srprismMemory', '1500'])
args.func_main(args)
expectedOut = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.bmtagger.bam')
assert_equal_bam_reads(self, outBam, expectedOut)
def test_bmtagger_empty_output(self):
empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
in_bam = os.path.join(util.file.get_test_input_path(),
'TestDepleteHuman', 'test-reads-human.bam')
out_bam = util.file.mkstempfname('-out.bam')
args = taxon_filter.parser_deplete_bam_bmtagger(
argparse.ArgumentParser()).parse_args([
in_bam, self.database_prefix_path, out_bam, '--srprismMemory',
'1500'
])
args.func_main(args)
assert_equal_bam_reads(self, out_bam, empty_bam)
def test_deplete_bmtagger_bam(self):
inBam = os.path.join(util.file.get_test_input_path(),
'TestDepleteHuman', 'test-reads.bam')
outBam = util.file.mkstempfname('-out.bam')
args = taxon_filter.parser_deplete_bam_bmtagger(
argparse.ArgumentParser()).parse_args(
[inBam, self.database_prefix_path, outBam])
args.func_main(args)
expectedOut = os.path.join(util.file.get_test_input_path(),
'TestDepleteHuman', 'expected',
'test-reads.bmtagger.bam')
assert_equal_bam_reads(self, outBam, expectedOut)
def test_bmtagger_empty_input(self):
os.environ.pop('TMPDIR', None)
util.file.set_tmp_dir(None)
empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
out_bam = util.file.mkstempfname('-out.bam')
args = taxon_filter.parser_deplete_bam_bmtagger(
argparse.ArgumentParser()).parse_args([
empty_bam, self.database_prefix_path, out_bam,
'--srprismMemory', '1500'
])
args.func_main(args)
assert_equal_bam_reads(self, out_bam, empty_bam)
def test_deplete_bmtagger_tar_db(self):
inBam = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam')
outBam = util.file.mkstempfname('-out.bam')
tar_db_tgz = util.file.mkstempfname('.db.tar.gz')
cmd = ['tar', '-C', os.path.dirname(self.database_prefix_path), '-cvzf', tar_db_tgz, '.']
subprocess.check_call(cmd)
args = taxon_filter.parser_deplete_bam_bmtagger(argparse.ArgumentParser()).parse_args([
inBam, tar_db_tgz, outBam, '--srprismMemory', '1500'])
args.func_main(args)
expectedOut = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.bmtagger.bam')
assert_equal_bam_reads(self, outBam, expectedOut)
os.unlink(tar_db_tgz)
def test_deplete_bmtagger_fasta_db(self):
inBam = os.path.join(util.file.get_test_input_path(),
'TestDepleteHuman', 'test-reads.bam')
ref_fasta = os.path.join(util.file.get_test_input_path(),
'5kb_human_from_chr6.fasta')
outBam = util.file.mkstempfname('-out.bam')
args = taxon_filter.parser_deplete_bam_bmtagger(
argparse.ArgumentParser()).parse_args(
[inBam, ref_fasta, outBam, '--srprismMemory', '1500'])
args.func_main(args)
expectedOut = os.path.join(util.file.get_test_input_path(),
'TestDepleteHuman', 'expected',
'test-reads.bmtagger.bam')
assert_equal_bam_reads(self, outBam, expectedOut)
def test_deplete_bmtagger_bam(self):
os.environ.pop('TMPDIR', None)
util.file.set_tmp_dir(None)
inBam = os.path.join(util.file.get_test_input_path(),
'TestDepleteHuman', 'test-reads.bam')
outBam = util.file.mkstempfname('-out.bam')
args = taxon_filter.parser_deplete_bam_bmtagger(
argparse.ArgumentParser()).parse_args([
inBam, self.database_prefix_path, outBam, '--srprismMemory',
'1500'
])
args.func_main(args)
expectedOut = os.path.join(util.file.get_test_input_path(),
'TestDepleteHuman', 'expected',
'test-reads.bmtagger.bam')
assert_equal_bam_reads(self, outBam, expectedOut)
def test_deplete_bmtagger_tar_db(self):
inBam = os.path.join(util.file.get_test_input_path(),
'TestDepleteHuman', 'test-reads.bam')
outBam = util.file.mkstempfname('-out.bam')
tar_db_tgz = util.file.mkstempfname('.db.tar.gz')
cmd = [
'tar', '-C',
os.path.dirname(self.database_prefix_path), '-cvzf', tar_db_tgz,
'.'
]
subprocess.check_call(cmd)
args = taxon_filter.parser_deplete_bam_bmtagger(
argparse.ArgumentParser()).parse_args(
[inBam, tar_db_tgz, outBam, '--srprismMemory', '1500'])
args.func_main(args)
expectedOut = os.path.join(util.file.get_test_input_path(),
'TestDepleteHuman', 'expected',
'test-reads.bmtagger.bam')
assert_equal_bam_reads(self, outBam, expectedOut)
os.unlink(tar_db_tgz)
