def test_deplete_empty(self):
myInputDir = util.file.get_test_input_path(self)
empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
# Run deplete_human
args = taxon_filter.parser_deplete_human(argparse.ArgumentParser()).parse_args(
[
empty_bam,
# output files
os.path.join(self.tempDir, 'deplete-empty.bmtagger.bam'),
os.path.join(self.tempDir, 'deplete-empty.rmdup.bam'),
os.path.join(self.tempDir, 'deplete-empty.blastn.bam'),
"--taxfiltBam", os.path.join(self.tempDir, 'deplete-empty.taxfilt.bam'),
# DBs
"--blastDbs", self.blastdb_path,
"--bmtaggerDbs", self.database_prefix_path,
"--lastDb", self.lastdb_path,
"--threads", "4"
]
)
args.func_main(args)
# Compare to expected
for fname in [
'deplete-empty.bmtagger.bam',
'deplete-empty.rmdup.bam', 'deplete-empty.blastn.bam',
'deplete-empty.taxfilt.bam'
]:
assert_equal_bam_reads(self, os.path.join(self.tempDir, fname), empty_bam)
def test_deplete_human(self):
myInputDir = util.file.get_test_input_path(self)
# Run deplete_human
args = taxon_filter.parser_deplete_human(
argparse.ArgumentParser()).parse_args([
os.path.join(myInputDir, 'test-reads.bam'),
# output files
os.path.join(self.tempDir, 'test-reads.bmtagger.bam'),
os.path.join(self.tempDir, 'test-reads.rmdup.bam'),
os.path.join(self.tempDir, 'test-reads.blastn.bam'),
"--taxfiltBam",
os.path.join(self.tempDir, 'test-reads.taxfilt.imperfect.bam'),
# DBs
"--blastDbs",
self.blastdb_path,
"--bmtaggerDbs",
self.database_prefix_path,
"--lastDb",
self.lastdb_path,
"--threads",
"4"
])
args.func_main(args)
# Compare to expected
for fname in [
'test-reads.bmtagger.bam', 'test-reads.rmdup.bam',
'test-reads.blastn.bam', 'test-reads.taxfilt.imperfect.bam'
]:
assert_equal_bam_reads(self, os.path.join(self.tempDir, fname),
os.path.join(myInputDir, 'expected', fname))
def test_blastn_empty_input(self):
empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
out_bam = util.file.mkstempfname('-out.bam')
taxon_filter.multi_db_deplete_bam(empty_bam, [self.blastdb_path],
taxon_filter.deplete_blastn_bam,
out_bam)
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, '--srprismMemory', '1500'])
args.func_main(args)
assert_equal_bam_reads(self, out_bam, empty_bam)
def test_deplete_human_aligned_input(self):
myInputDir = util.file.get_test_input_path(self)
# Run deplete_human
args = taxon_filter.parser_deplete(argparse.ArgumentParser()).parse_args(
[
os.path.join(myInputDir, 'test-reads-aligned.bam'),
# output files
os.path.join(self.tempDir, 'test-reads.revert.bam'),
os.path.join(self.tempDir, 'test-reads.bwa.bam'),
os.path.join(self.tempDir, 'test-reads.bmtagger.bam'),
os.path.join(self.tempDir, 'test-reads.blastn.bam'),
# DBs
"--blastDbs", self.blastdb_path,
"--bmtaggerDbs", self.database_prefix_path,
"--srprismMemory", '1500',
]
)
args.func_main(args)
# Compare to expected
for fname in [
'test-reads.revert.bam',
'test-reads.bwa.bam',
'test-reads.bmtagger.bam',
'test-reads.blastn.bam'
]:
assert_equal_bam_reads(self, os.path.join(self.tempDir, fname), os.path.join(myInputDir, 'aligned-expected', fname))
def test_deplete_human(self):
os.environ.pop('TMPDIR', None)
util.file.set_tmp_dir(None)
myInputDir = util.file.get_test_input_path(self)
# Run deplete_human
args = taxon_filter.parser_deplete_human(
argparse.ArgumentParser()).parse_args([
os.path.join(myInputDir, 'test-reads.bam'),
# output files
os.path.join(self.tempDir, 'test-reads.bmtagger.bam'),
os.path.join(self.tempDir, 'test-reads.rmdup.bam'),
os.path.join(self.tempDir, 'test-reads.blastn.bam'),
# DBs
"--blastDbs",
self.blastdb_path,
"--bmtaggerDbs",
self.database_prefix_path,
"--chunkSize",
"0",
"--srprismMemory",
'1500',
"--threads",
str(_CPUS)
])
args.func_main(args)
# Compare to expected
for fname in [
'test-reads.bmtagger.bam',
'test-reads.rmdup.bam',
'test-reads.blastn.bam',
]:
assert_equal_bam_reads(self, os.path.join(self.tempDir, fname),
os.path.join(myInputDir, 'expected', fname))
def test_deplete_human_aligned_input(self):
myInputDir = util.file.get_test_input_path(self)
# Run deplete_human
args = taxon_filter.parser_deplete_human(argparse.ArgumentParser()).parse_args(
[
os.path.join(myInputDir, 'test-reads-aligned.bam'),
# output files
os.path.join(self.tempDir, 'test-reads.revert.bam'),
os.path.join(self.tempDir, 'test-reads.bmtagger.bam'),
os.path.join(self.tempDir, 'test-reads.rmdup.bam'),
os.path.join(self.tempDir, 'test-reads.blastn.bam'),
"--taxfiltBam", os.path.join(self.tempDir, 'test-reads.taxfilt.imperfect.bam'),
# DBs
"--blastDbs", self.blastdb_path,
"--bmtaggerDbs", self.database_prefix_path,
"--lastDb", self.lastdb_path,
"--threads", "4"
]
)
args.func_main(args)
# Compare to expected
for fname in [
'test-reads.revert.bam', 'test-reads.bmtagger.bam',
'test-reads.rmdup.bam', 'test-reads.blastn.bam',
'test-reads.taxfilt.imperfect.bam'
]:
assert_equal_bam_reads(self, os.path.join(self.tempDir, fname), os.path.join(myInputDir, 'aligned-expected', fname))
def test_deplete_empty(self):
empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
# Run deplete_human
args = taxon_filter.parser_deplete(argparse.ArgumentParser()).parse_args(
[
empty_bam,
# output files
os.path.join(self.tempDir, 'deplete-empty.revert.bam'),
os.path.join(self.tempDir, 'deplete-empty.bwa.bam'),
os.path.join(self.tempDir, 'deplete-empty.bmtagger.bam'),
os.path.join(self.tempDir, 'deplete-empty.blastn.bam'),
# DBs
"--blastDbs", self.blastdb_path,
"--bmtaggerDbs", self.database_prefix_path,
"--srprismMemory", '1500',
]
)
args.func_main(args)
# Compare to expected
for fname in [
'deplete-empty.bmtagger.bam', 'deplete-empty.blastn.bam',
]:
assert_equal_bam_reads(self, os.path.join(self.tempDir, fname), empty_bam)
def test_deplete_human(self):
myInputDir = util.file.get_test_input_path(self)
# Run deplete_human
args = taxon_filter.parser_deplete(argparse.ArgumentParser()).parse_args(
[
os.path.join(myInputDir, 'test-reads.bam'),
# output files
os.path.join(self.tempDir, 'test-reads.revert.bam'),
os.path.join(self.tempDir, 'test-reads.bwa.bam'),
os.path.join(self.tempDir, 'test-reads.bmtagger.bam'),
os.path.join(self.tempDir, 'test-reads.rmdup.bam'),
os.path.join(self.tempDir, 'test-reads.blastn.bam'),
# DBs
"--blastDbs", self.blastdb_path,
"--bmtaggerDbs", self.database_prefix_path,
"--chunkSize", "0",
"--srprismMemory", '1500',
]
)
args.func_main(args)
# Compare to expected
for fname in [
'test-reads.revert.bam',
'test-reads.bwa.bam',
'test-reads.bmtagger.bam',
'test-reads.rmdup.bam',
'test-reads.blastn.bam'
]:
assert_equal_bam_reads(self, os.path.join(self.tempDir, fname), os.path.join(myInputDir, 'expected', fname))
def test_deplete_empty(self):
empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
# Run deplete_human
args = taxon_filter.parser_deplete(argparse.ArgumentParser()).parse_args(
[
empty_bam,
# output files
os.path.join(self.tempDir, 'deplete-empty.revert.bam'),
os.path.join(self.tempDir, 'deplete-empty.bwa.bam'),
os.path.join(self.tempDir, 'deplete-empty.bmtagger.bam'),
os.path.join(self.tempDir, 'deplete-empty.rmdup.bam'),
os.path.join(self.tempDir, 'deplete-empty.blastn.bam'),
# DBs
"--blastDbs", self.blastdb_path,
"--bmtaggerDbs", self.database_prefix_path,
"--srprismMemory", '1500',
]
)
args.func_main(args)
# Compare to expected
for fname in [
'deplete-empty.bmtagger.bam',
'deplete-empty.rmdup.bam', 'deplete-empty.blastn.bam',
]:
assert_equal_bam_reads(self, os.path.join(self.tempDir, fname), empty_bam)
def test_lastal_unbuilt_db(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')
outBam = util.file.mkstempfname('-out-taxfilt.bam')
taxon_filter.filter_lastal_bam(in_bam, self.polio_fasta, outBam)
assert_equal_bam_reads(self, outBam, empty_bam)
def test_filter_lastal_bam_polio(self):
inBam = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.blastn.bam')
outBam = util.file.mkstempfname('-out-taxfilt.bam')
args = taxon_filter.parser_filter_lastal_bam(argparse.ArgumentParser()).parse_args([
inBam, self.lastdb_path, outBam])
args.func_main(args)
expectedOut = os.path.join(util.file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.taxfilt.imperfect.bam')
assert_equal_bam_reads(self, outBam, expectedOut)
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_lastal_empty_input(self):
empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
outBam = util.file.mkstempfname('-out-taxfilt.bam')
taxon_filter.filter_lastal_bam(
empty_bam,
self.lastdb_path,
outBam
)
assert_equal_bam_reads(self, outBam, empty_bam)
def test_lastal_unbuilt_db(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')
outBam = util.file.mkstempfname('-out-taxfilt.bam')
taxon_filter.filter_lastal_bam(
in_bam,
self.polio_fasta,
outBam
)
assert_equal_bam_reads(self, outBam, 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_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_human(self):
myInputDir = util.file.get_test_input_path(self)
tempDir = tempfile.mkdtemp()
ref_fasta = os.path.join(myInputDir, '5kb_human_from_chr6.fasta')
database_prefix_path = os.path.join(tempDir, "5kb_human_from_chr6")
# create blast db
blastdb_path = tools.blast.MakeblastdbTool().build_database(
ref_fasta, database_prefix_path)
# create bmtagger db
bmtooldb_path = tools.bmtagger.BmtoolTool().build_database(
ref_fasta, database_prefix_path + ".bitmask")
srprismdb_path = tools.bmtagger.SrprismTool().build_database(
ref_fasta, database_prefix_path + ".srprism")
# create last db
lastdb_path = tools.last.Lastdb().build_database(
ref_fasta, database_prefix_path)
# Run deplete_human
args = taxon_filter.parser_deplete_human(
argparse.ArgumentParser()).parse_args([
os.path.join(myInputDir, 'test-reads.bam'),
# output files
os.path.join(tempDir, 'test-reads.revert.bam'),
os.path.join(tempDir, 'test-reads.bmtagger.bam'),
os.path.join(tempDir, 'test-reads.rmdup.bam'),
os.path.join(tempDir, 'test-reads.blastn.bam'),
"--taxfiltBam",
os.path.join(tempDir, 'test-reads.taxfilt.bam'),
# DBs
"--blastDbs",
blastdb_path,
"--bmtaggerDbs",
database_prefix_path,
"--lastDb",
lastdb_path,
"--threads",
"4"
])
args.func_main(args)
# Compare to expected
for fname in [
'test-reads.revert.bam', 'test-reads.bmtagger.bam',
'test-reads.rmdup.bam', 'test-reads.blastn.bam',
'test-reads.taxfilt.bam'
]:
assert_equal_bam_reads(self, os.path.join(tempDir, fname),
os.path.join(myInputDir, 'expected', fname))
def test_filter_lastal_bam_polio(self):
inBam = os.path.join(util.file.get_test_input_path(),
'TestDepleteHuman', 'expected',
'test-reads.blastn.bam')
outBam = util.file.mkstempfname('-out-taxfilt.bam')
args = taxon_filter.parser_filter_lastal_bam(
argparse.ArgumentParser()).parse_args(
[inBam, self.lastdb_path, outBam])
args.func_main(args)
expectedOut = os.path.join(util.file.get_test_input_path(),
'TestDepleteHuman', 'expected',
'test-reads.taxfilt.imperfect.bam')
assert_equal_bam_reads(self, outBam, expectedOut)
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_fastq_bam(self):
myInputDir = util.file.get_test_input_path(self)
# Define file names
inFastq1 = os.path.join(myInputDir, 'in1.fastq')
inFastq2 = os.path.join(myInputDir, 'in2.fastq')
inHeader = os.path.join(myInputDir, 'inHeader.txt')
expected1_7Sam = os.path.join(myInputDir, 'expected.java1_7.sam')
expected1_8Sam = os.path.join(myInputDir, 'expected.java1_8.sam')
expected1_8Sam_v15 = os.path.join(myInputDir,
'expected.java1_8_v1.5.sam')
expectedFastq1 = os.path.join(myInputDir, 'expected.fastq1')
outBamCmd = util.file.mkstempfname('.bam')
outBamTxt = util.file.mkstempfname('.bam')
outSam = util.file.mkstempfname('.sam')
outFastq1 = util.file.mkstempfname('.fastq')
outFastq2 = util.file.mkstempfname('.fastq')
outHeader = util.file.mkstempfname('.txt')
outHeaderFix = util.file.mkstempfname('.fix.txt')
# in1.fastq, in2.fastq -> out.bam; header params from command-line
parser = read_utils.parser_fastq_to_bam(argparse.ArgumentParser())
args = parser.parse_args([
inFastq1,
inFastq2,
outBamCmd,
'--sampleName',
'FreeSample',
'--JVMmemory',
'1g',
'--picardOptions',
'LIBRARY_NAME=Alexandria',
'PLATFORM=9.75',
'SEQUENCING_CENTER=KareemAbdul-Jabbar',
])
args.func_main(args)
alternate_expected_vals = {"VN": ["1.4", "1.5", "1.6", "1.7"]}
self.assertEqualSamHeaders(
outBamCmd,
expected1_7Sam,
other_allowed_values=alternate_expected_vals)
assert_equal_bam_reads(self, outBamCmd, expected1_7Sam)
parser = read_utils.parser_fastq_to_bam(argparse.ArgumentParser())
args = parser.parse_args(
[inFastq1, inFastq2, outBamTxt, '--header', inHeader])
args.func_main(args)
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_human(self):
myInputDir = util.file.get_test_input_path(self)
tempDir = tempfile.mkdtemp()
ref_fasta = os.path.join(myInputDir, '5kb_human_from_chr6.fasta')
database_prefix_path = os.path.join(tempDir, "5kb_human_from_chr6")
# create blast db
blastdb_path = tools.blast.MakeblastdbTool().build_database(ref_fasta, database_prefix_path)
# create bmtagger db
bmtooldb_path = tools.bmtagger.BmtoolTool().build_database(ref_fasta, database_prefix_path + ".bitmask")
srprismdb_path = tools.bmtagger.SrprismTool().build_database(ref_fasta, database_prefix_path + ".srprism")
# create last db
lastdb_path = tools.last.Lastdb().build_database(ref_fasta, database_prefix_path)
# Run deplete_human
args = taxon_filter.parser_deplete_human(argparse.ArgumentParser()).parse_args(
[
os.path.join(myInputDir, 'test-reads.bam'),
# output files
os.path.join(tempDir, 'test-reads.revert.bam'),
os.path.join(tempDir, 'test-reads.bmtagger.bam'),
os.path.join(tempDir, 'test-reads.rmdup.bam'),
os.path.join(tempDir, 'test-reads.blastn.bam'),
"--taxfiltBam",
os.path.join(tempDir, 'test-reads.taxfilt.bam'),
# DBs
"--blastDbs",
blastdb_path,
"--bmtaggerDbs",
database_prefix_path,
"--lastDb",
lastdb_path,
"--threads",
"4"
]
)
args.func_main(args)
# Compare to expected
for fname in [
'test-reads.revert.bam', 'test-reads.bmtagger.bam', 'test-reads.rmdup.bam', 'test-reads.blastn.bam',
'test-reads.taxfilt.bam'
]:
assert_equal_bam_reads(self, os.path.join(tempDir, fname), os.path.join(myInputDir, 'expected', fname))
def test_bam_filter_by_tax_id(self):
temp_dir = tempfile.gettempdir()
input_dir = util.file.get_test_input_path(self)
taxonomy_dir = os.path.join(util.file.get_test_input_path(),
"TestMetagenomicsSimple", "db", "taxonomy")
filtered_bam = util.file.mkstempfname('.bam')
args = [
os.path.join(input_dir, "input.bam"),
os.path.join(input_dir, "input.kraken-reads.tsv.gz"), filtered_bam,
os.path.join(taxonomy_dir, "nodes.dmp"),
os.path.join(taxonomy_dir, "names.dmp"), "--taxIDs", "186538"
]
args = metagenomics.parser_filter_bam_to_taxa(
argparse.ArgumentParser()).parse_args(args)
args.func_main(args)
expected_bam = os.path.join(input_dir, "expected.bam")
assert_equal_bam_reads(self, filtered_bam, expected_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_bam_filter_by_tax_id(self):
temp_dir = tempfile.gettempdir()
input_dir = util.file.get_test_input_path(self)
taxonomy_dir = os.path.join(util.file.get_test_input_path(),"TestMetagenomicsSimple","db","taxonomy")
filtered_bam = util.file.mkstempfname('.bam')
args = [
os.path.join(input_dir,"input.bam"),
os.path.join(input_dir,"input.kraken-reads.tsv.gz"),
filtered_bam,
os.path.join(taxonomy_dir,"nodes.dmp"),
os.path.join(taxonomy_dir,"names.dmp"),
"--taxIDs",
"186538"
]
args = metagenomics.parser_filter_bam_to_taxa(argparse.ArgumentParser()).parse_args(args)
args.func_main(args)
expected_bam = os.path.join(input_dir,"expected.bam")
assert_equal_bam_reads(self, filtered_bam, expected_bam)
def test_deplete_blastn_bam(self):
tempDir = tempfile.mkdtemp()
myInputDir = util.file.get_test_input_path(self)
# Run deplete_blastn_bam
inBam = os.path.join(myInputDir, 'in.bam')
outBam = os.path.join(tempDir, 'out.bam')
args = taxon_filter.parser_deplete_blastn_bam(
argparse.ArgumentParser()).parse_args([inBam] +
self.blastdbs_multi +
[outBam, "--chunkSize", "0"])
args.func_main(args)
# samtools view for out.sam and compare to expected
outSam = os.path.join(tempDir, 'out.sam')
samtools = tools.samtools.SamtoolsTool()
samtools.view(['-h'], outBam, outSam)
assert_equal_bam_reads(self, outSam,
os.path.join(myInputDir, 'expected.sam'))
def test_lastal_empty_input(self):
empty_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
outBam = util.file.mkstempfname('-out-taxfilt.bam')
taxon_filter.filter_lastal_bam(empty_bam, self.lastdb_path, outBam)
assert_equal_bam_reads(self, outBam, empty_bam)
