def _call_cleanup(self,
input_fp,
output_dir,
params,
job_prefix,
poll_directly,
suppress_submit_jobs):
""" Called as the last step in __call__.
"""
if poll_directly:
if params['observation_metadata_fp'] is not None:
observation_metadata = \
parse_observation_metadata(
open(params['observation_metadata_fp'], 'U'))
else:
observation_metadata = None
biom_fp = join(output_dir, 'observation_table.biom')
biom_table = make_otu_table(
open(join(output_dir, 'observation_map.txt'), 'U'),
observation_metadata)
write_biom_table(biom_table, biom_fp)
else:
# can't construct the final biom file if not polling
# directly as the final observation map won't have been created yet
pass
def _call_cleanup(self,
input_fp,
output_dir,
params,
job_prefix,
poll_directly,
suppress_submit_jobs):
""" Called as the last step in __call__.
"""
if poll_directly:
if params['observation_metadata_fp'] is not None:
observation_metadata = \
parse_observation_metadata(
open(params['observation_metadata_fp'], 'U'))
else:
observation_metadata = None
biom_fp = join(output_dir, 'observation_table.biom')
biom_table = make_otu_table(
open(join(output_dir, 'observation_map.txt'), 'U'),
observation_metadata)
write_biom_table(biom_table, biom_fp)
else:
# can't construct the final biom file if not polling
# directly as the final observation map won't have been created yet
pass
def _call_cleanup(self, input_fp, output_dir, params, job_prefix, poll_directly, suppress_submit_jobs):
""" Called as the last step in __call__.
"""
if poll_directly:
if params["observation_metadata_fp"] != None:
observation_metadata = parse_observation_metadata(open(params["observation_metadata_fp"], "U"))
else:
observation_metadata = None
biom_fp = join(output_dir, "observation_table.biom")
biom_f = open(biom_fp, "w")
biom_f.write(make_otu_table(open(join(output_dir, "observation_map.txt"), "U"), observation_metadata))
biom_f.close()
else:
# can't construct the final biom file if not polling
# directly as the final observation map won't have been created yet
pass