INNER CODE UNIT · Python
predict_taxonomy
BigDataBiology/SemiBin · SemiBin/main.py:718
def predict_taxonomy(logger, contig_fasta, cannot_name,
taxonomy_results_fname, GTDB_reference, num_process,
binned_length, must_link_threshold, output):
"""
Predict taxonomy using mmseqs and generate cannot-link file
contig_fasta: contig file used
GTDB_reference: GTDB path
cannot_name: name for cannot-link constraint
binned_short: threshold for contigs used in binning
must_link_threshold: threshold of contigs for must-link constraints
"""
import tempfile
with tempfile.TemporaryDirectory() as tdir:
filtered_fasta = os.path.join(tdir, 'SemiBinFiltered.fa')
namelist = []
num_must_link = 0