def test_coverage_get_from_sam(metagenome, sam_alignment, tmp_path): out = tmp_path / "covs_from_sam.tsv" df = coverage.get(fasta=metagenome, from_spades=False, out=out, sam=sam_alignment) assert df.index.name == "contig" assert "coverage" in df.columns assert out.exists()
def test_coverage_get_from_reads(metagenome, fwd_reads, rev_reads, tmp_path): out = tmp_path / "covs_from_bed.tsv" df = coverage.get( fasta=metagenome, from_spades=False, out=out, fwd_reads=fwd_reads, rev_reads=rev_reads, ) assert df.index.name == "contig" assert "coverage" in df.columns assert out.exists()
def test_embed_df_already_exists(metagenome, df_exists_fpath, bed_alignment): coverage.get(fasta=metagenome, out=df_exists_fpath, bed=bed_alignment)
def test_get_not_enough_passed_arguments(metagenome, tmp_path): out = tmp_path / "covs.tsv" with pytest.raises(ValueError): coverage.get(fasta=metagenome, from_spades=False, out=out)
def test_coverage_get_from_spades(metagenome, tmp_path): out = tmp_path / "covs_from_spades.tsv" df = coverage.get(fasta=metagenome, from_spades=True, out=out) assert df.index.name == "contig" assert "coverage" in df.columns assert out.exists()