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()