def cluster_closed_reference(sequences: QIIME1DemuxFormat,
reference_database: NinjaOpsDBDirFmt) \
-> (BIOMV100Format, QIIME1DemuxFormat):
# Input paths supplied to ninja.py.
sequences_fp = str(sequences)
reference_database_dir = os.path.join(str(reference_database), 'db')
# Output directory to store ninja.py results.
output_dirfmt = model.DirectoryFormat()
output_dir = str(output_dirfmt)
cmd = [
'ninja.py', '--input', sequences_fp, '--database',
reference_database_dir, '--output', output_dir, '--full_output'
]
run_command(cmd)
biom_fp = os.path.join(output_dir, 'ninja_otutable.biom')
output_biom_fmt = BIOMV100Format(biom_fp, mode='r')
# Keep a reference to the DirectoryFormat this BIOM file resides in so that
# the directory isn't deleted when `output_dirfmt` goes out of scope upon
# function exit. The directory will be cleaned up appropriately when
# `output_biom_fmt` is cleaned up and avoids copying the BIOM file.
output_biom_fmt.__dirfmt = output_dirfmt
# Get the set of IDs that failed to hit the reference database.
failed_ids = set()
failed_ids_fp = os.path.join(output_dir, 'ninja_fail.txt')
with open(failed_ids_fp, 'r') as fh:
for line in fh:
id = line.rstrip('\n')
failed_ids.add(id)
# Filter the input sequences to only those that failed to hit the reference
# database.
output_failures_fmt = QIIME1DemuxFormat()
with output_failures_fmt.open() as fh:
for seq in skbio.io.read(sequences_fp, format='fasta'):
id = seq.metadata['id']
if id in failed_ids:
# Turning off roundtripping options to speed up writing. We can
# safely turn these options off because we know the sequence
# IDs are rountrip-safe since we're reading them from a FASTA
# file.
#
# http://scikit-bio.org/docs/latest/generated/
# skbio.io.format.fasta.html#writer-specific-parameters
seq.write(fh,
id_whitespace_replacement=None,
description_newline_replacement=None)
return output_biom_fmt, output_failures_fmt
def test_file_format_validate_negative(self):
for file in self.negatives:
filepath = self.get_data_path('qiime1-demux-format/%s' % file)
with self.assertRaisesRegex(ValidationError, 'QIIME1DemuxFormat'):
QIIME1DemuxFormat(filepath, mode='r').validate()
def test_file_format_validate_positive(self):
for file in self.positives:
filepath = self.get_data_path('qiime1-demux-format/%s' % file)
QIIME1DemuxFormat(filepath, mode='r').validate()