def test_kaiju(mocker):
p = mocker.patch('tools.kaiju.Kaiju.classify')
args = [
'input.bam',
'db.fmi',
'tax_db',
'output.report',
'--outReads', 'output.reads',
]
args = metagenomics.parser_kaiju(argparse.ArgumentParser()).parse_args(args)
args.func_main(args)
p.assert_called_with('db.fmi', 'tax_db', 'input.bam', output_report='output.report', num_threads=mock.ANY, output_reads='output.reads')
def test_kaiju(mocker):
p = mocker.patch('tools.kaiju.Kaiju.classify')
args = [
'input.bam',
'db.fmi',
'tax_db',
'output.report',
'--outReads', 'output.reads',
]
args = metagenomics.parser_kaiju(argparse.ArgumentParser()).parse_args(args)
args.func_main(args)
p.assert_called_with('db.fmi', 'tax_db', 'input.bam', output_report='output.report', num_threads=mock.ANY, output_reads='output.reads')
def test_kaiju(kaiju_db, krona_db, taxonomy_db, input_bam):
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads')
cmd = [
input_bam, kaiju_db, taxonomy_db, out_report, '--outReads', out_reads
]
parser = metagenomics.parser_kaiju(argparse.ArgumentParser())
args = parser.parse_args(cmd)
args.func_main(args)
assert os.path.getsize(out_report) > 0
assert os.path.getsize(out_reads) > 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 kaiju_db:
zaire_found = False
tai_found = False
for line in report_lines:
if len(line) < 2:
continue
if 'Zaire ebolavirus' in line[-2] and float(line[0]) > 40:
zaire_found = True
elif 'Tai Forest' in line[-2]:
tai_found = True
assert zaire_found
assert not tai_found
out_html = util.file.mkstempfname('.krona.html')
parser = metagenomics.parser_krona(argparse.ArgumentParser())
args = parser.parse_args(
['--inputType', 'kaiju', out_report, krona_db, out_html])
args.func_main(args)
if 'TestMetagenomicsSimple' in kaiju_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_kaiju(kaiju_db, krona_db, taxonomy_db, input_bam):
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads')
cmd = [input_bam, kaiju_db, taxonomy_db, out_report, '--outReads', out_reads]
parser = metagenomics.parser_kaiju(argparse.ArgumentParser())
args = parser.parse_args(cmd)
args.func_main(args)
assert os.path.getsize(out_report) > 0
assert os.path.getsize(out_reads) > 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 kaiju_db:
zaire_found = False
tai_found = False
for line in report_lines:
if len(line) < 2:
continue
if 'Zaire ebolavirus' in line[-2] and float(line[0]) > 40:
zaire_found = True
elif 'Tai Forest' in line[-2]:
tai_found = True
assert zaire_found
assert not tai_found
out_html = util.file.mkstempfname('.krona.html')
parser = metagenomics.parser_krona(argparse.ArgumentParser())
args = parser.parse_args(['--inputType', 'kaiju', out_report, krona_db, out_html])
args.func_main(args)
if 'TestMetagenomicsSimple' in kaiju_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_kaiju(kaiju_db, krona_db, taxonomy_db, input_bam):
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads')
cmd = [
input_bam, kaiju_db, taxonomy_db, out_report, '--outReads', out_reads
]
parser = metagenomics.parser_kaiju(argparse.ArgumentParser())
args = parser.parse_args(cmd)
args.func_main(args)
assert os.path.getsize(out_report) > 0
assert os.path.getsize(out_reads) > 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 kaiju_db:
zaire_found = False
tai_found = False
for line in report_lines:
if len(line) < 2:
continue
if 'Zaire ebolavirus' in line[-2] and float(line[0]) > 40:
zaire_found = True
elif 'Tai Forest' in line[-2]:
tai_found = True
assert zaire_found
assert not tai_found
out_html = util.file.mkstempfname('.krona.html')
parser = metagenomics.parser_krona(argparse.ArgumentParser())
args = parser.parse_args(
['--inputType', 'kaiju', out_report, krona_db, out_html])
args.func_main(args)
''' well... this doesn't actually find Zaire ebolavirus!