"""
Unit and regression test for the choppa package.
"""
# Import package, test suite, and other packages as needed
import sys
import pytest
[docs]
def test_choppa_imported():
"""Sample test, will always pass so long as import statement worked."""
assert "choppa" in sys.modules
from choppa.data.toy_data.resources import (
TOY_COMPLEX,
TOY_FITNESS_DATA_COMPLETE,
TOY_FITNESS_DATA_TRUNCATED,
)
from choppa.data.toy_data.resources import (
TOY_FITNESS_DATA_SECTIONED,
TOY_FITNESS_DATA_COMPLETE_NOCONF,
)
from choppa.IO.input import FitnessFactory, ComplexFactory
from choppa.align import AlignFactory
from choppa import render
[docs]
def test_choppa_render_toy_mac1_sectioned(tmp_path):
"""Tests that `choppa` is able to render views on a fitness dataset that
has poor (fractioned) overlap with a toy PDB file."""
fitness_dict = FitnessFactory(
TOY_FITNESS_DATA_SECTIONED, confidence_colname="confidence"
).get_fitness_basedict()
complex = ComplexFactory(TOY_COMPLEX).load_pdb()
complex_rdkit = ComplexFactory(TOY_COMPLEX).load_pdb_rdkit()
filled_aligned_fitness_dict = AlignFactory(fitness_dict, complex).align_fitness()
# also test that we're actually reproducing the PDB sequence in the alignment.
# prevents us from accidentally writing out the wrong logoplots.
alignment = [
resdict["wildtype"] for _, resdict in filled_aligned_fitness_dict.items()
]
assert "".join([val.pop() for val in alignment[:4]]) == "SFSG"
assert "".join([val["aa"] for val in alignment[6:25]]) == "KLTDNVYIKNADIVEEAKK"
render.PublicationView(
filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.pse"
).render()
render.InteractiveView(
filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.html"
).render()
# we know the intended output, test on this.
assert len(filled_aligned_fitness_dict) == 164
assert 4 not in filled_aligned_fitness_dict
assert 5 in filled_aligned_fitness_dict
# check files exist
assert (tmp_path / "test.pse").exists()
assert (tmp_path / "test.html").exists()
[docs]
def test_choppa_correct_custom_columns():
"""Tests that `choppa` is able to read in correct columns in input fitness data."""
fitness_dict = FitnessFactory(TOY_FITNESS_DATA_SECTIONED).get_fitness_basedict()
# check that some of the correct keys are in the dict
assert "fitness_csv_index" in fitness_dict[5]
assert "wildtype" in fitness_dict[5]
assert "mutants" in fitness_dict[5]
# test that one of the residues has the intended number of mutants
assert len(fitness_dict[5]["wildtype"]) == 3
assert len(fitness_dict[5]["mutants"]) == 20
[docs]
def test_choppa_incorrect_custom_columns():
"""Tests that `choppa` throws an error for incorrectly specified columns in input fitness data."""
with pytest.raises(KeyError, match="not found in"):
FitnessFactory(
TOY_FITNESS_DATA_SECTIONED,
wildtype_colname="foo",
mutant_colname="foo",
fitness_colname="foo",
resindex_colname="foo",
).get_fitness_basedict()
[docs]
def test_choppa_render_toy_mac1_sectioned_noconf(tmp_path):
"""Tests that `choppa` is able to render views on a fitness dataset that
has poor (fractioned) overlap with a toy PDB file, while not adding confidence."""
fitness_dict = FitnessFactory(TOY_FITNESS_DATA_SECTIONED).get_fitness_basedict()
complex = ComplexFactory(TOY_COMPLEX).load_pdb()
complex_rdkit = ComplexFactory(TOY_COMPLEX).load_pdb_rdkit()
filled_aligned_fitness_dict = AlignFactory(fitness_dict, complex).align_fitness()
render.PublicationView(
filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.pse"
).render()
render.InteractiveView(
filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.html"
).render()
assert len(filled_aligned_fitness_dict) == 164
# check files exist
assert (tmp_path / "test.pse").exists()
assert (tmp_path / "test.html").exists()
[docs]
def test_choppa_render_toy_mac1_full(tmp_path):
"""Tests that `choppa` is able to render views on a fitness dataset that
has complete overlap with a toy PDB file."""
fitness_dict = FitnessFactory(
TOY_FITNESS_DATA_COMPLETE, confidence_colname="confidence"
).get_fitness_basedict()
complex = ComplexFactory(TOY_COMPLEX).load_pdb()
complex_rdkit = ComplexFactory(TOY_COMPLEX).load_pdb_rdkit()
filled_aligned_fitness_dict = AlignFactory(fitness_dict, complex).align_fitness()
render.PublicationView(
filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.pse"
).render()
render.InteractiveView(
filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.html"
).render()
assert len(filled_aligned_fitness_dict) == 164
# check files exist
assert (tmp_path / "test.pse").exists()
assert (tmp_path / "test.html").exists()
[docs]
def test_choppa_render_toy_mac1_truncated(tmp_path):
"""Tests that `choppa` is able to render views on a fitness dataset that
has decenr (trunacted at either end) overlap with a toy PDB file."""
fitness_dict = FitnessFactory(
TOY_FITNESS_DATA_TRUNCATED, confidence_colname="confidence"
).get_fitness_basedict()
complex = ComplexFactory(TOY_COMPLEX).load_pdb()
complex_rdkit = ComplexFactory(TOY_COMPLEX).load_pdb_rdkit()
filled_aligned_fitness_dict = AlignFactory(fitness_dict, complex).align_fitness()
render.PublicationView(
filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.pse"
).render()
render.InteractiveView(
filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.html"
).render()
assert len(filled_aligned_fitness_dict) == 164
# check files exist
assert (tmp_path / "test.pse").exists()
assert (tmp_path / "test.html").exists()