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):
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):
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_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)
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_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))
