def get_bloom_sequences():
"""Get the filepath to the bloom sequences
Returns
-------
str
The filepath to the bloom sequences
Raises
------
IOError
If the path does not exist
"""
repo = get_repository_dir()
return get_existing_path(os.path.join(repo, 'data/AG/BLOOM.fasta'))
def get_bloom_sequences():
"""Get the filepath to the bloom sequences
Returns
-------
str
The filepath to the bloom sequences
Raises
------
IOError
If the path does not exist
"""
repo = get_repository_dir()
return get_existing_path(os.path.join(repo, 'data/AG/BLOOM.fasta'))
def get_reference_set():
"""Get the reference set to use for OTU picking
Returns
-------
str
The file path to the reference sequences.
str
The file path to the reference taxonomy.
"""
if ag.is_test_env():
repo = get_repository_dir()
ref_seqs = os.path.join(repo, 'tests/data/otus.fna')
ref_tax = os.path.join(repo, 'tests/data/otus.txt')
return ref_seqs, ref_tax
else:
return qdr.get_reference_sequences(), qdr.get_reference_taxonomy()
def get_reference_set():
"""Get the reference set to use for OTU picking
Returns
-------
str
The file path to the reference sequences.
str
The file path to the reference taxonomy.
"""
if ag.is_test_env():
repo = get_repository_dir()
ref_seqs = os.path.join(repo, 'tests/data/otus.fna')
ref_tax = os.path.join(repo, 'tests/data/otus.txt')
return ref_seqs, ref_tax
else:
return qdr.get_reference_sequences(), qdr.get_reference_taxonomy()
def _stage_test_accessions():
"""Stage test data
Notes
-----
Staging copies the test dataset into the working directory. This "tricks"
the fetch_study mechanism as it'll appear that the data have already been
sourced from EBI.
"""
repo = get_repository_dir()
for acc in _TEST_ACCESSIONS:
src = os.path.join(repo, 'tests/data/%s' % acc)
dst = os.path.join(ag.WORKING_DIR, '01/%s' % acc)
if not os.path.exists(os.path.join(ag.WORKING_DIR, '01')):
os.mkdir('01')
shutil.copytree(src, dst)
def _stage_test_accessions():
"""Stage test data
Notes
-----
Staging copies the test dataset into the working directory. This "tricks"
the fetch_study mechanism as it'll appear that the data have already been
sourced from EBI.
"""
repo = get_repository_dir()
for acc in _TEST_ACCESSIONS:
src = os.path.join(repo, 'tests/data/%s' % acc)
dst = os.path.join(ag.WORKING_DIR, '01/%s' % acc)
if not os.path.exists(os.path.join(ag.WORKING_DIR, '01')):
os.mkdir('01')
shutil.copytree(src, dst)
def _get_data(data_dir, tag):
"""Get a non-AG table and mapping file
Parameters
----------
data_dir : str
The base data path
tag : str
The filetag (e.g., HMPv35_100nt)
Returns
-------
(str, str)
The filepath to the table, and the filepath to the mapping file.
Notes
-----
If $AG_TESTING == 'True', then the data returned will correspond to the
test dataset.
Raises
------
IOError
If the filepaths are not accessible
"""
repo = get_repository_dir()
data = 'tests/data' if ag.is_test_env() else 'data'
base = os.path.join(repo, data)
table = os.path.join(base, data_dir, '%s.biom' % tag)
mapping = os.path.join(base, data_dir, '%s.txt' % tag)
if not os.path.exists(table):
raise IOError("Unable to access: %s" % table)
if not os.path.exists(mapping):
raise IOError("Unable to access: %s" % table)
return table, mapping
def _get_data(data_dir, tag):
"""Get a non-AG table and mapping file
Parameters
----------
data_dir : str
The base data path
tag : str
The filetag (e.g., HMPv35_100nt)
Returns
-------
(str, str)
The filepath to the table, and the filepath to the mapping file.
Notes
-----
If $AG_TESTING == 'True', then the data returned will correspond to the
test dataset.
Raises
------
IOError
If the filepaths are not accessible
"""
repo = get_repository_dir()
data = 'tests/data' if ag.is_test_env() else 'data'
base = os.path.join(repo, data)
table = os.path.join(base, data_dir, '%s.biom' % tag)
mapping = os.path.join(base, data_dir, '%s.txt' % tag)
if not os.path.exists(table):
raise IOError("Unable to access: %s" % table)
if not os.path.exists(mapping):
raise IOError("Unable to access: %s" % table)
return table, mapping