def _assign_taxonomy(self, extracted_reads, assignment_method):
graftm_align_directory_base = os.path.join(self._working_directory,
'graftm_aligns')
os.mkdir(graftm_align_directory_base)
commands = []
all_tmp_files = []
# Run each one at a time serially so that the number of threads is
# respected, to save RAM as one DB needs to be loaded at once, and so
# fewer open files are needed, so that the open file count limit is
# eased.
for singlem_package, readsets in extracted_reads.each_package_wise():
tmp_files = []
for readset in readsets:
if len(readset.sequences) > 0:
tmp = tempfile.NamedTemporaryFile(prefix='singlem.%s' %
readset.sample_name,
suffix=".fasta")
# Record basename (remove .fasta) so that the graftm output
# file is recorded for later on in pipe.
tmpbase = os.path.basename(tmp.name[:-6])
readset.tmpfile_basename = tmpbase
seqio = SequenceIO()
seqio.write_fasta(readset.sequences, tmp)
tmp.flush()
tmp_files.append(tmp)
if len(tmp_files) > 0:
tmpnames = list([tg.name for tg in tmp_files])
cmd = "%s "\
"--threads %i "\
"--forward %s "\
"--graftm_package %s "\
"--output_directory %s/%s "\
"--max_samples_for_krona 0 "\
"--assignment_method %s" % (
self._graftm_command_prefix(singlem_package.is_protein_package()),
self._num_threads,
' '.join(tmpnames),
singlem_package.graftm_package_path(),
graftm_align_directory_base,
singlem_package.graftm_package_basename(),
assignment_method)
commands.append(cmd)
all_tmp_files.append(tmp_files)
extern.run_many(commands, num_threads=1)
for tmp_files in all_tmp_files:
[t.close() for t in tmp_files]
logging.info("Finished running taxonomic assignment with GraftM")
return SingleMPipeTaxonomicAssignmentResult(
graftm_align_directory_base)
def _test_package(self, package_path):
'''Give a GraftM package a spin, and see if it works in reality with default
parameters (i.e. pplacer). If it does not work, then raise an error.
Parameters
----------
package_path: str
path to graftm_package to be tested
'''
pkg = GraftMPackage.acquire(package_path)
with tempdir.TempDir() as graftM_graft_test_dir_name:
# Take a subset of sequences for testing
with tempfile.NamedTemporaryFile(suffix=".fa") as tf:
seqio = SequenceIO()
seqio.write_fasta(
itertools.islice(seqio.each_sequence(open(pkg.unaligned_sequence_database_path())), 10),
tf)
tf.flush()
cmd = "graftM graft --forward %s --graftm_package %s --output_directory %s --force" %(
tf.name, package_path, graftM_graft_test_dir_name)
extern.run(cmd)
def _test_package(self, package_path):
'''Give a GraftM package a spin, and see if it works in reality with default
parameters (i.e. pplacer). If it does not work, then raise an error.
Parameters
----------
package_path: str
path to graftm_package to be tested
'''
pkg = GraftMPackage.acquire(package_path)
with tempdir.TempDir() as graftM_graft_test_dir_name:
# Take a subset of sequences for testing
with tempfile.NamedTemporaryFile(suffix=".fa", mode='w') as tf:
seqio = SequenceIO()
with open(pkg.unaligned_sequence_database_path()) as f:
seqio.write_fasta(
itertools.islice(seqio.each_sequence(f), 10), tf)
tf.flush()
cmd = "graftM graft --forward %s --graftm_package %s --output_directory %s --force" % (
tf.name, package_path, graftM_graft_test_dir_name)
extern.run(cmd)