def test_krakenuniq(krakenuniq_db, input_bam):
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads.gz')
cmd = [
krakenuniq_db, input_bam, '--outReports', out_report, '--outReads',
out_reads
]
parser = metagenomics.parser_krakenuniq(argparse.ArgumentParser())
args = parser.parse_args(cmd)
args.func_main(args)
with util.file.open_or_gzopen(out_reads, 'r') as inf:
assert len(inf.read()) > 0
with util.file.open_or_gzopen(out_report) as inf:
report_lines = [x.strip().split('\t') for x in inf.readlines()]
report_lines = [x for x in report_lines if x]
assert is_gz_file(out_reads)
assert os.path.getsize(out_report) > 0
if 'TestMetagenomicsSimple' in krakenuniq_db:
zaire_found = False
tai_found = False
for line in report_lines:
if 'Zaire ebolavirus' in line[-1] and float(line[0]) > 90:
zaire_found = True
elif 'Tai Forest' in line[-1]:
tai_found = True
assert zaire_found
assert not tai_found
def test_krakenuniq_on_empty(krakenuniq_db, input_bam):
if 'TestMetagenomicsViralMix' not in krakenuniq_db:
return
input_bam = join(util.file.get_test_input_path(), 'empty.bam')
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads.gz')
cmd = [
krakenuniq_db, input_bam, '--outReport', out_report, '--outReads',
out_reads
]
parser = metagenomics.parser_krakenuniq(argparse.ArgumentParser())
args = parser.parse_args(cmd)
args.func_main(args)
with util.file.open_or_gzopen(out_reads, 'r') as inf:
assert len(inf.read()) == 0
assert is_gz_file(out_reads)
with open(out_report, 'rt') as inf:
lines = [
line.strip() for line in inf.readlines()
if not line.startswith('#') and not line.startswith('%')
]
out_report_contents = [line for line in lines if line]
assert len(out_report_contents) == 1
assert out_report_contents[0].split('\t') == [
'100.00', '0', '0', '0', '0', 'NA', '0', 'no rank', 'unclassified'
]
def test_krakenuniq_krona(krakenuniq_db, krona_db, input_bam):
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads.gz')
cmd = [
krakenuniq_db, input_bam, '--outReport', out_report, '--outReads',
out_reads
]
parser = metagenomics.parser_krakenuniq(argparse.ArgumentParser())
args = parser.parse_args(cmd)
args.func_main(args)
out_html = util.file.mkstempfname('.krona.html')
parser = metagenomics.parser_krona(argparse.ArgumentParser())
args = parser.parse_args(
['--inputType', 'krakenuniq', out_report, krona_db, out_html])
args.func_main(args)
if 'TestMetagenomicsSimple' in krakenuniq_db:
ebola_found = False
cleaner = lxml.html.clean.Cleaner(remove_unknown_tags=False,
page_structure=False)
tree = cleaner.clean_html(lxml.html.parse(out_html))
root_node = tree.xpath('//krona/node')[0]
for n in root_node.iterdescendants():
if n.get('name') == 'Zaire ebolavirus':
if int(n.xpath('magnitude/val')[0].text) > 0:
ebola_found = True
assert ebola_found
def test_krakenuniq(mocker):
p = mocker.patch('tools.kraken.KrakenUniq.pipeline')
args = [
'db',
'input.bam',
'--outReports', 'output.report',
'--outReads', 'output.reads',
]
args = metagenomics.parser_krakenuniq(argparse.ArgumentParser()).parse_args(args)
args.func_main(args)
p.assert_called_with('db', ['input.bam'], num_threads=mock.ANY, filter_threshold=mock.ANY, out_reports=['output.report'], out_reads=['output.reads'])
def test_krakenuniq(mocker):
p = mocker.patch('tools.kraken.KrakenUniq.pipeline')
args = [
'db',
'input.bam',
'--outReports', 'output.report',
'--outReads', 'output.reads',
]
args = metagenomics.parser_krakenuniq(argparse.ArgumentParser()).parse_args(args)
args.func_main(args)
p.assert_called_with('db', ['input.bam'], num_threads=mock.ANY, filter_threshold=mock.ANY, out_reports=['output.report'], out_reads=['output.reads'])
def test_krakenuniq_krona(krakenuniq_db, krona_db, input_bam):
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads.gz')
cmd = [
krakenuniq_db, input_bam, '--outReport', out_report, '--outReads',
out_reads
]
parser = metagenomics.parser_krakenuniq(argparse.ArgumentParser())
args = parser.parse_args(cmd)
args.func_main(args)
out_html = util.file.mkstempfname('.krona.html')
parser = metagenomics.parser_krona(argparse.ArgumentParser())
args = parser.parse_args(
['--inputType', 'krakenuniq', out_report, krona_db, out_html])
args.func_main(args)
''' well... this doesn't actually find Zaire ebolavirus!