def test_basic():
params = {'-g': join(INPATH, 'map_red.tsv'),
'-t': join(INPATH, 'go-basic.obo.1'),
'-o': join(OUTPATH, 'output.tsv')}
response = runner.invoke(_propagate_GO, f"{dict2str(params)}")
assert response.exit_code == 0
genes_out = load_df(join(OUTPATH, "output.tsv"))
genes_exp = load_df(join(EXPPATH, "new_tree_propagated_GO.tsv"))
pdt.assert_frame_equal(genes_out, genes_exp)
def test_basic():
params = {
'-i': join(INPATH, 'deepfri_reduced.tsv'),
'-g': join(INPATH, 'GO_informative.txt'),
'-o': join(OUTPATH, 'output.tsv')
}
response = runner.invoke(_process_deepfri, f"{dict2str(params)}")
assert response.exit_code == 0
genes_out = load_df(join(OUTPATH, "output.tsv"))
genes_exp = load_df(join(EXPPATH, "deepfri_out.tsv"))
pdt.assert_frame_equal(genes_out, genes_exp)
def test_missing_checkm_and_gtdb():
params = {
'-r': join(INPATH, 'cluster_genes/nr.reduced.clstr'),
'-g': join(INPATH, 'cluster_genes/sample_genes.fa'),
'-c': join(INPATH, 'assemble/merged.min500.contigs.fa'),
'-b': join(INPATH, 'metabat2/'),
'-t': join(INPATH, 'empty/'), # difference wrt basic
'-m': join(INPATH, 'empty/'), # difference wrt basic
'-e': join(INPATH, 'eggnog-mapper/eggNOG_reduced.tsv'),
'-p': join(OUTPATH),
'-o': 'example_split'
}
response = runner.invoke(_perform_mapping, f"{dict2str(params)}")
assert response.exit_code == 0
out = load_df(join(OUTPATH, f"example_split.tsv"))
exp = load_df(join(EXPPATH, f"table_missing_checkm_gtdb.tsv"))
pdt.assert_frame_equal(out, exp)
def test_missing_checkm_and_gtdb():
params = {
'-r': join(INPATH, 'cluster_genes/nr.reduced.clstr'),
'-g': join(INPATH, 'cluster_genes/sample_genes.fa'),
'-c': join(INPATH, 'assemble/merged.min500.contigs.fa'),
'-b': join(INPATH, 'metabat2/'),
'-t': join(INPATH, 'empty/'), # difference wrt basic
'-m': join(INPATH, 'empty/'), # difference wrt basic
'-e': join(INPATH, 'eggnog-mapper/eggNOG_reduced.tsv'),
'-o': join(OUTPATH)
}
response = runner.invoke(_perform_mapping, f"{dict2str(params)}")
assert response.exit_code == 0
for name in ['Mapped_genes_cluster', 'Individual_mapped_genes', 'MAGS']:
out = load_df(os.path.join(OUTPATH, f"{name}.tsv"))
exp = load_df(os.path.join(EXPPATH, f"{name}_missing_checkm_gtdb.tsv"))
pdt.assert_frame_equal(out, exp)
def test_basic_split():
params = {
'-r': join(INPATH, 'cluster_genes/nr.reduced.clstr'),
'-g': join(INPATH, 'cluster_genes/sample_genes.fa'),
'-c': join(INPATH, 'assemble/merged.min500.contigs.fa'),
'-b': join(INPATH, 'metabat2/'),
'-t': join(INPATH, 'gtdbtk/'),
'-m': join(INPATH, 'checkm/'),
'-e': join(INPATH, 'eggnog-mapper/eggNOG_reduced.tsv'),
'-s': '',
'-p': join(OUTPATH),
'-o': 'example_split'
}
response = runner.invoke(_perform_mapping, f"{dict2str(params)}")
assert response.exit_code == 0
for name in ['mapped_genes_cluster', 'individual_mapped_genes', 'MAGS']:
out = load_df(join(OUTPATH, f"example_split_{name}.tsv"))
exp = load_df(join(EXPPATH, f"{name}.tsv"))
pdt.assert_frame_equal(out, exp)