def test_isovar_result_str():
for result in run_isovar(
variants=data_path("data/b16.f10/b16.vcf"),
alignment_file=data_path("data/b16.f10/b16.combined.sorted.bam")):
s = str(result)
assert len(s) > 0
assert s.startswith("IsovarResult(")
assert s.endswith(")")
def test_isovar_main_to_dataframe():
results = run_isovar(
variants=data_path("data/b16.f10/b16.vcf"),
alignment_file=data_path("data/b16.f10/b16.combined.sorted.bam"))
df = isovar_results_to_dataframe(results)
print(df)
eq_(len(df), 4)
# B16 test data has 2/4 variants with enough coverage
# to translate protein sequences
eq_(df["passes_all_filters"].sum(), 2)
def test_isovar_result_property_types():
for result in run_isovar(
variants=data_path("data/b16.f10/b16.vcf"),
alignment_file=data_path("data/b16.f10/b16.combined.sorted.bam")):
# variant
assert type(result.variant) is Variant
# counts of genes and transcripts from variant
assert type(result.num_overlapping_genes) is int
assert type(result.num_overlapping_coding_genes) is int
assert type(result.num_overlapping_transcripts) is int
assert type(result.num_overlapping_coding_transcripts) is int
# protein sequence
assert type(result.top_protein_sequence) in (type(None),
ProteinSequence)
# counts of genes and transcripts from protein sequences
assert type(result.num_genes_from_protein_sequences) is int
assert type(result.num_genes_from_top_protein_sequence) is int
assert type(result.num_transcripts_from_protein_sequences) is int
assert type(result.num_transcripts_from_top_protein_sequence) is int
# read and fragment counts
assert type(result.num_ref_reads) is int
assert type(result.num_alt_reads) is int
assert type(result.num_other_reads) is int
assert type(result.num_ref_fragments) is int
assert type(result.num_alt_fragments) is int
assert type(result.num_other_fragments) is int
# read and fragment fractions
assert type(result.fraction_ref_reads) is float
assert type(result.fraction_alt_reads) is float
assert type(result.fraction_other_reads) is float
assert type(result.fraction_ref_fragments) is float
assert type(result.fraction_alt_fragments) is float
assert type(result.fraction_other_fragments) is float
# read and fragment count ratios
assert type(result.ratio_alt_to_other_reads) is float
assert type(result.ratio_alt_to_other_fragments) is float
assert type(result.ratio_other_to_alt_fragments) is float
assert type(result.ratio_other_to_alt_reads) is float
assert type(result.ratio_ref_to_other_fragments) is float
assert type(result.ratio_other_to_ref_fragments) is float
assert type(result.ratio_other_to_ref_reads) is float
# this property aggregates all filters
assert result.passes_all_filters in {True, False}
assert type(result.protein_sequence_mutation_start) in (int,
type(None))
assert type(result.protein_sequence_mutation_end) in (int, type(None))
def test_isovar_result_nonsyn_variants():
for result in run_isovar(
variants=data_path("data/b16.f10/b16.vcf"),
alignment_file=data_path("data/b16.f10/b16.combined.sorted.bam")):
print(result.variant)
print(result.predicted_effect)
if result.has_mutant_protein_sequence_from_rna:
assert result.num_amino_acid_mismatches_from_predicted_effect is not None
assert result.num_amino_acid_mismatches_from_reference is not None
assert result.num_amino_acid_mismatches_from_reference > 0
eq_(result.protein_sequence_matches_reference, False)
eq_(result.protein_sequence_contains_mutation, True)
else:
assert result.num_amino_acid_mismatches_from_predicted_effect is None
assert result.num_amino_acid_mismatches_from_reference is None
assert result.protein_sequence_matches_predicted_mutation_effect is None
assert result.protein_sequence_matches_reference is None
assert result.protein_sequence_contains_mutation is None
def test_isovar_result_clone_with_updates():
for result in run_isovar(
variants=data_path("data/b16.f10/b16.vcf"),
alignment_file=data_path("data/b16.f10/b16.combined.sorted.bam")):
result2 = result.clone_with_updates(variant=None)
assert result != result2
def test_isovar_result_clone():
for result in run_isovar(
variants=data_path("data/b16.f10/b16.vcf"),
alignment_file=data_path("data/b16.f10/b16.combined.sorted.bam")):
result2 = result.clone()
eq_(result, result2)