From 6edd40a9420d98f0bc46691730239ef9a5aefc23 Mon Sep 17 00:00:00 2001 From: gbouras13 Date: Mon, 18 Sep 2023 20:54:07 +0930 Subject: [PATCH] pyrodigal tests add threads --- tests/test_external_commands.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/tests/test_external_commands.py b/tests/test_external_commands.py index 6ddda6c..834bd2b 100644 --- a/tests/test_external_commands.py +++ b/tests/test_external_commands.py @@ -15,7 +15,7 @@ from loguru import logger from bin.processes import (run_aragorn, run_mash_sketch, run_minced, - run_phanotate, run_pyrodigal) + run_phanotate, run_pyrodigal, run_pyrodigal_gv) # import functions from bin.util import remove_directory @@ -49,19 +49,27 @@ def test_run_pyrodigal(self): fasta: Path = f"{standard_data}/SAOMS1.fasta" coding_table = 11 meta = False - run_pyrodigal(fasta, standard_data_output, meta, coding_table) # meta = False + threads = 2 + run_pyrodigal(fasta, standard_data_output, meta, coding_table, threads) # meta = False def test_run_pyrodigal_meta(self): fasta: Path = f"{standard_data}/SAOMS1.fasta" coding_table = 11 meta = True - run_pyrodigal(fasta, standard_data_output, meta, coding_table) # meta = False + threads = 2 + run_pyrodigal(fasta, standard_data_output, meta, coding_table, threads) # meta = False def test_run_pyrodigal_c4(self): fasta: Path = f"{standard_data}/SAOMS1.fasta" coding_table = 4 meta = False - run_pyrodigal(fasta, standard_data_output, meta, coding_table) # meta = False + threads = 2 + run_pyrodigal(fasta, standard_data_output, meta, coding_table, threads) # meta = False + + def test_run_pyrodigal_gv(self): + fasta: Path = f"{standard_data}/SAOMS1.fasta" + threads = 2 + run_pyrodigal_gv(fasta, standard_data_output, threads) # meta = False def test_run_minced(self): fasta: Path = f"{standard_data}/SAOMS1.fasta"