def main():
args = parser.parse_args()
input_biom_fp = args.input_biom_fp
output_biom_fp = args.output_biom_fp
merged_fastq_fp = args.merged_fastq_fp
deblur_biom = load_table(input_biom_fp)
if output_biom_fp is None:
output_biom_fp = os.path.splitext(input_biom_fp)[0] + '.merged.biom'
with open(merged_fastq_fp) as fq:
merged_fastq = readfq(fq)
# read each of the fastqs, make a dict of label:merged read
merge_dict = get_merged_dict(merged_fastq)
# filter biom to just the keys of dict
deblur_biom = deblur_biom.filter(lambda val, id_, md: id_ in merge_dict,
axis='observation')
output_biom = collapse_biom_observations(deblur_biom, merge_dict)
with biom_open(output_biom_fp, 'w') as f:
output_biom.to_hdf5(f, 'deblur_relabel_merged.py')
def main():
args = parser.parse_args()
input_biom_fp = args.input_biom_fp
output_biom_fp = args.output_biom_fp
merged_fastq_fp = args.merged_fastq_fp
deblur_biom = load_table(input_biom_fp)
if output_biom_fp is None:
output_biom_fp = os.path.splitext(input_biom_fp)[0] + '.merged.biom'
with open(merged_fastq_fp) as fq:
merged_fastq = readfq(fq)
# read each of the fastqs, make a dict of label:merged read
merge_dict = get_merged_dict(merged_fastq)
# filter biom to just the keys of dict
deblur_biom = deblur_biom.filter(
lambda val, id_, md: id_ in merge_dict, axis='observation')
output_biom = collapse_biom_observations(deblur_biom, merge_dict)
with biom_open(output_biom_fp, 'w') as f:
output_biom.to_hdf5(f, 'deblur_relabel_merged.py')
def main():
args = parser.parse_args()
input_biom_fp = args.input_biom_fp
output_biom_fp = args.output_biom_fp
output_fasta_fp = args.output_fasta_fp
metadata_name = args.metadata_name
name_stub = args.name_stub
test = args.test
if test:
run_unittests()
return(0)
deblur_biom = load_table(input_biom_fp)
if output_biom_fp is None:
output_biom_fp = os.path.splitext(input_biom_fp)[0] + '.renamed.biom'
output_biom = rename_deblur_biom(deblur_biom, name_stub=name_stub, metadata_name=metadata_name)
if output_fasta_fp is not None:
fasta = format_seqs_from_deblur_biom(output_biom, metadata_name=metadata_name)
with open(output_fasta_fp, 'w') as f:
f.write(fasta)
with biom_open(output_biom_fp, 'w') as f:
output_biom.to_hdf5(f, 'deblur_relabel_merged.py')
def test_json_to_hdf5_collapsed_samples(self):
"""Correctly converts json to HDF5 changing the sample metadata"""
with biom_open(self.json_collapsed_samples) as f:
obs = self.cmd(table=parse_biom_table(f),
output_filepath=self.output_filepath,
to_hdf5=True,
collapsed_samples=True)
obs = load_table(self.output_filepath)
exp = Table(np.array([[0., 1.], [6., 6.], [6., 1.], [1., 4.], [0.,
2.]]),
observation_ids=[
u'GG_OTU_1', u'GG_OTU_2', u'GG_OTU_3', u'GG_OTU_4',
u'GG_OTU_5'
],
sample_ids=[u'skin', u'gut'],
observation_metadata=[{
u'taxonomy': [
u'k__Bacteria', u'p__Proteobacteria',
u'c__Gammaproteobacteria', u'o__Enterobacteriales',
u'f__Enterobacteriaceae', u'g__Escherichia', u's__'
]
}, {
u'taxonomy': [
u'k__Bacteria', u'p__Cyanobacteria',
u'c__Nostocophycideae', u'o__Nostocales',
u'f__Nostocaceae', u'g__Dolichospermum', u's__'
]
}, {
u'taxonomy': [
u'k__Archaea', u'p__Euryarchaeota',
u'c__Methanomicrobia', u'o__Methanosarcinales',
u'f__Methanosarcinaceae', u'g__Methanosarcina',
u's__'
]
}, {
u'taxonomy': [
u'k__Bacteria', u'p__Firmicutes', u'c__Clostridia',
u'o__Halanaerobiales', u'f__Halanaerobiaceae',
u'g__Halanaerobium',
u's__Halanaerobiumsaccharolyticum'
]
}, {
u'taxonomy': [
u'k__Bacteria', u'p__Proteobacteria',
u'c__Gammaproteobacteria', u'o__Enterobacteriales',
u'f__Enterobacteriaceae', u'g__Escherichia', u's__'
]
}],
sample_metadata=[{
u'collapsed_ids': [u'Sample4', u'Sample5', u'Sample6']
}, {
u'collapsed_ids': [u'Sample1', u'Sample2', u'Sample3']
}],
type=u'OTU table')
self.assertEqual(obs, exp)
def test_json_to_hdf5_collapsed_metadata(self):
"""Correctly converts json to HDF5 changing the observation metadata"""
with biom_open(self.json_collapsed_obs) as f:
t = parse_biom_table(f)
obs = self.cmd(table=t,
output_filepath=self.output_filepath, to_hdf5=True,
collapsed_observations=True)
obs = load_table(self.output_filepath)
exp = Table(np.array([[2., 1., 1., 0., 0., 1.],
[0., 0., 1., 4., 0., 2.],
[5., 1., 0., 2., 3., 1.],
[0., 1., 2., 0., 0., 0.]]),
observation_ids=[u'p__Firmicutes', u'p__Euryarchaeota',
u'p__Cyanobacteria',
u'p__Proteobacteria'],
sample_ids=[u'Sample1', u'Sample2', u'Sample3',
u'Sample4', u'Sample5', u'Sample6'],
observation_metadata=[
{u'collapsed_ids': [u'GG_OTU_4']},
{u'collapsed_ids': [u'GG_OTU_3']},
{u'collapsed_ids': [u'GG_OTU_2']},
{u'collapsed_ids': [u'GG_OTU_1', u'GG_OTU_5']}],
sample_metadata=[
{u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CGCTTATCGAGA',
u'Description': u'human gut',
u'BODY_SITE': u'gut'},
{u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CATACCAGTAGC',
u'Description': u'human gut',
u'BODY_SITE': u'gut'},
{u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CTCTCTACCTGT',
u'Description': u'human gut',
u'BODY_SITE': u'gut'},
{u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CTCTCGGCCTGT',
u'Description': u'human skin',
u'BODY_SITE': u'skin'},
{u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CTCTCTACCAAT',
u'Description': u'human skin',
u'BODY_SITE': u'skin'},
{u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CTAACTACCAAT',
u'Description': u'human skin',
u'BODY_SITE': u'skin'}],
type=u'OTU table')
self.assertEqual(obs, exp)
def test_json_to_hdf5_collapsed_samples(self):
"""Correctly converts json to HDF5 changing the sample metadata"""
with biom_open(self.json_collapsed_samples) as f:
obs = self.cmd(table=parse_biom_table(f),
output_filepath=self.output_filepath, to_hdf5=True,
collapsed_samples=True)
obs = load_table(self.output_filepath)
exp = Table(np.array([[0., 1.], [6., 6.], [6., 1.],
[1., 4.], [0., 2.]]),
observation_ids=[u'GG_OTU_1', u'GG_OTU_2', u'GG_OTU_3',
u'GG_OTU_4', u'GG_OTU_5'],
sample_ids=[u'skin', u'gut'],
observation_metadata=[
{u'taxonomy': [u'k__Bacteria', u'p__Proteobacteria',
u'c__Gammaproteobacteria',
u'o__Enterobacteriales',
u'f__Enterobacteriaceae',
u'g__Escherichia', u's__']},
{u'taxonomy': [u'k__Bacteria', u'p__Cyanobacteria',
u'c__Nostocophycideae',
u'o__Nostocales', u'f__Nostocaceae',
u'g__Dolichospermum', u's__']},
{u'taxonomy': [u'k__Archaea', u'p__Euryarchaeota',
u'c__Methanomicrobia',
u'o__Methanosarcinales',
u'f__Methanosarcinaceae',
u'g__Methanosarcina', u's__']},
{u'taxonomy': [u'k__Bacteria', u'p__Firmicutes',
u'c__Clostridia', u'o__Halanaerobiales',
u'f__Halanaerobiaceae',
u'g__Halanaerobium',
u's__Halanaerobiumsaccharolyticum']},
{u'taxonomy': [u'k__Bacteria', u'p__Proteobacteria',
u'c__Gammaproteobacteria',
u'o__Enterobacteriales',
u'f__Enterobacteriaceae',
u'g__Escherichia', u's__']}],
sample_metadata=[
{u'collapsed_ids': [u'Sample4', u'Sample5',
u'Sample6']},
{u'collapsed_ids': [u'Sample1', u'Sample2',
u'Sample3']}
],
type=u'OTU table')
self.assertEqual(obs, exp)
def test_json_to_hdf5_collapsed_metadata(self):
"""Correctly converts json to HDF5 changing the observation metadata"""
with biom_open(self.json_collapsed_obs) as f:
t = parse_biom_table(f)
obs = self.cmd(table=t,
output_filepath=self.output_filepath,
to_hdf5=True,
collapsed_observations=True)
obs = load_table(self.output_filepath)
exp = Table(np.array([[2., 1., 1., 0., 0.,
1.], [0., 0., 1., 4., 0., 2.],
[5., 1., 0., 2., 3., 1.],
[0., 1., 2., 0., 0., 0.]]),
observation_ids=[
u'p__Firmicutes', u'p__Euryarchaeota',
u'p__Cyanobacteria', u'p__Proteobacteria'
],
sample_ids=[
u'Sample1', u'Sample2', u'Sample3', u'Sample4',
u'Sample5', u'Sample6'
],
observation_metadata=[{
u'collapsed_ids': [u'GG_OTU_4']
}, {
u'collapsed_ids': [u'GG_OTU_3']
}, {
u'collapsed_ids': [u'GG_OTU_2']
}, {
u'collapsed_ids': [u'GG_OTU_1', u'GG_OTU_5']
}],
sample_metadata=[{
u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CGCTTATCGAGA',
u'Description': u'human gut',
u'BODY_SITE': u'gut'
}, {
u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CATACCAGTAGC',
u'Description': u'human gut',
u'BODY_SITE': u'gut'
}, {
u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CTCTCTACCTGT',
u'Description': u'human gut',
u'BODY_SITE': u'gut'
}, {
u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CTCTCGGCCTGT',
u'Description': u'human skin',
u'BODY_SITE': u'skin'
}, {
u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CTCTCTACCAAT',
u'Description': u'human skin',
u'BODY_SITE': u'skin'
}, {
u'LinkerPrimerSequence': u'CATGCTGCCTCCCGTAGGAGT',
u'BarcodeSequence': u'CTAACTACCAAT',
u'Description': u'human skin',
u'BODY_SITE': u'skin'
}],
type=u'OTU table')
self.assertEqual(obs, exp)
