def test_kraken_fifo(kraken_db):
in_bams = list(os.path.join(util.file.get_test_input_path(), d, 'test-reads.bam') for d in ('TestMetagenomicsSimple', 'TestMetagenomicsViralMix'))
out_reports = list(util.file.mkstempfname('.out_{}.report.txt'.format(i)) for i in (1,2))
out_reads = list(util.file.mkstempfname('.out_{}.reads.txt.gz'.format(i)) for i in (1,2))
with util.file.fifo(names=('inbam1.bam', 'inbam2.bam')) as (inbam1, inbam2):
with open(inbam1, 'wb') as b1, open(inbam2, 'wb') as b2:
p1 = subprocess.Popen(['cat', in_bams[0]], stdout=b1)
p2 = subprocess.Popen(['cat', in_bams[1]], stdout=b2)
cmd = [kraken_db, inbam1, inbam2] \
+ ['--outReports'] + out_reports \
+ ['--outReads'] + out_reads
parser = metagenomics.parser_kraken(argparse.ArgumentParser())
args = parser.parse_args(cmd)
args.func_main(args)
print("waiting for kraken to drain fifo for first bam file")
p1.wait()
print("waiting for kraken to drain fifo for second bam file")
p2.wait()
# just check for non-empty outputs
for outfile in out_reads:
with util.file.open_or_gzopen(outfile, 'r') as inf:
assert len(inf.read()) > 0
for outfile in out_reports:
with util.file.open_or_gzopen(outfile) as inf:
assert len(inf.read()) > 0
def test_kraken(kraken_db, input_bam):
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads.gz')
cmd = [input_bam, kraken_db, '--outReport', out_report, '--outReads', out_reads]
parser = metagenomics.parser_kraken(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() for x in inf.readlines()]
assert os.path.getsize(out_report) > 0
if 'TestMetaegenomicsSimple' in kraken_db:
zaire_found = False
tai_found = False
for line in report_lines:
if line[-1] == 'Zaire ebolavirus' 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_kraken(kraken_db, input_bam):
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads.gz')
cmd = [input_bam, kraken_db, '--outReport', out_report, '--outReads', out_reads]
parser = metagenomics.parser_kraken(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
def test_kraken(kraken_db, input_bam):
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads.gz')
cmd = [
input_bam, kraken_db, '--outReport', out_report, '--outReads',
out_reads
]
parser = metagenomics.parser_kraken(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
def test_kraken_krona(tmpdir, kraken_db, krona_db, input_bam):
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads.gz')
cmd = [input_bam, kraken_db, '--outReport', out_report, '--outReads', out_reads]
parser = metagenomics.parser_kraken(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([out_reads, krona_db, out_html])
args.func_main(args)
def test_kraken_krona(kraken_db, krona_db, input_bam):
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads.gz')
cmd = [input_bam, kraken_db, '--outReport', out_report, '--outReads', out_reads]
parser = metagenomics.parser_kraken(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([out_reads, krona_db, out_html])
args.func_main(args)
def test_kraken(kraken_db, input_bam):
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads.gz')
cmd = [kraken_db, input_bam, '--outReports', out_report, '--outReads', out_reads]
parser = metagenomics.parser_kraken(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() for x in inf.readlines()]
assert os.path.getsize(out_report) > 0
'''
def kraken_db(request, tmpdir_module, kraken, db_type):
data_dir = join(util.file.get_test_input_path(), db_type)
db_dir = join(data_dir, 'db')
parser = metagenomics.parser_kraken(argparse.ArgumentParser())
db = os.path.join(tmpdir_module, 'kraken_db_{}'.format(db_type))
parser = metagenomics.parser_kraken_build(argparse.ArgumentParser())
cmd = [db, '--library', join(db_dir, 'library'),
'--taxonomy', join(db_dir, 'taxonomy'),
'--subsetTaxonomy',
'--minimizerLen', '10',
'--clean']
parser.parse_args(cmd)
args = parser.parse_args(cmd)
args.func_main(args)
return db
def test_kraken_on_empty(kraken_db, input_bam):
if 'TestMetagenomicsViralMix' not in kraken_db:
return
input_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
out_report = util.file.mkstempfname('.report')
out_reads = util.file.mkstempfname('.reads.gz')
cmd = [input_bam, kraken_db, '--outReport', out_report, '--outReads', out_reads]
parser = metagenomics.parser_kraken(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 open(out_report, 'rt') as inf:
out_report_contents = inf.readlines()
assert len(out_report_contents) == 1
out_report_contents = out_report_contents[0].rstrip('\n').split('\t')
assert out_report_contents == ['100.00', '0', '0', 'U', '0', 'unclassified']
def test_kraken_multi(kraken_db):
in_bams = list(os.path.join(util.file.get_test_input_path(), d, 'test-reads.bam') for d in ('TestMetagenomicsSimple', 'TestMetagenomicsViralMix'))
out_reports = list(util.file.mkstempfname('.out_{}.report.txt'.format(i)) for i in (1,2))
out_reads = list(util.file.mkstempfname('.out_{}.reads.txt.gz'.format(i)) for i in (1,2))
cmd = [kraken_db] + in_bams \
+ ['--outReports'] + out_reports \
+ ['--outReads'] + out_reads
parser = metagenomics.parser_kraken(argparse.ArgumentParser())
args = parser.parse_args(cmd)
args.func_main(args)
# just check for non-empty outputs
for outfile in out_reads:
with util.file.open_or_gzopen(outfile, 'r') as inf:
assert len(inf.read()) > 0
for outfile in out_reports:
with util.file.open_or_gzopen(outfile) as inf:
assert len(inf.read()) > 0
