Commit 9666df6e authored by Martin Larralde's avatar Martin Larralde
Browse files

Replace `add_nodes` with `Nodes.extract` in `connection_scoring` benchmark code

parent 7cec8f63
......@@ -8,7 +8,7 @@ import json
import tqdm
from pyrodigal import Nodes, Sequence
from pyrodigal._pyrodigal import METAGENOMIC_BINS, add_nodes, ConnectionScorer
from pyrodigal._pyrodigal import METAGENOMIC_BINS, ConnectionScorer
from pyrodigal.tests.fasta import parse
......@@ -40,7 +40,7 @@ for filename in tqdm.tqdm(glob.glob(os.path.join(args.data, "*.fna"))):
# create nodes
nodes = Nodes()
add_nodes(nodes, seq, tinf)
nodes.extract(seq, translation_table=tinf.translation_table)
# run connection scoring
for backend in ["avx", "sse", "generic", None]:
......
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