File size: 4,947 Bytes
5631464 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 | """Test haddock3-traceback client."""
import os
import shutil
from pathlib import Path
import tempfile
import pandas as pd
import pytest
from haddock.clis.cli_traceback import (
main,
get_steps_without_pdbs,
subset_traceback,
)
from . import golden_data
@pytest.fixture
def rigid_json():
"""Provide example rigidbody io.json file."""
return Path(golden_data, "io_rigid.json")
@pytest.fixture
def flexref_json():
"""Provide example flexref io.json file."""
return Path(golden_data, "io_flexref.json")
@pytest.fixture
def expected_traceback():
"Provide expected traceback dataframe."
exp_tr = [["00_topo1", "00_topo2", "1_rigidbody", "1_rigidbody_rank", "4_flexref", "4_flexref_rank"], # noqa: E501
["4G6K_fv_haddock.psf", "4I1B-matched_haddock.psf", "rigidbody_3.pdb", "1", "flexref_1.pdb", "1"], # noqa: E501
["4G6K_fv_haddock.psf", "4I1B-matched_haddock.psf", "rigidbody_1.pdb", "2", "flexref_2.pdb", "2"], # noqa: E501
["4G6K_fv_haddock.psf", "4I1B-matched_haddock.psf", "rigidbody_4.pdb", "3", "-", "-"], # noqa: E501
["4G6K_fv_haddock.psf", "4I1B-matched_haddock.psf", "rigidbody_2.pdb", "4", "-", "-"]] # noqa: E501
exp_tr_df = pd.DataFrame(exp_tr[1:], columns=exp_tr[0])
return exp_tr_df
def test_main(rigid_json, flexref_json, expected_traceback):
"""Test haddock3-traceback client."""
with tempfile.TemporaryDirectory() as tmpdir:
# build fake run_dir
run_dir = Path(tmpdir, "example_dir")
step_dirs = [os.path.join(run_dir, "1_rigidbody"),
os.path.join(run_dir, "4_flexref")]
# Loop over directories to be created
for d in [run_dir, *step_dirs]:
os.mkdir(d)
shutil.copy(rigid_json, os.path.join(step_dirs[0], "io.json"))
shutil.copy(flexref_json, os.path.join(step_dirs[1], "io.json"))
# create fake, empty pdb files
for i in range(1, 5):
open(os.path.join(step_dirs[0], f"rigidbody_{i}.pdb"), "w").close()
for i in range(1, 3):
open(os.path.join(step_dirs[1], f"flexref_{i}.pdb"), "w").close()
# run haddock3-traceback
main(run_dir)
# check traceback folder exists
assert os.path.isdir(os.path.join(run_dir, "traceback"))
# check traceback files exist
tr_file = os.path.join(run_dir, "traceback", "traceback.tsv")
assert os.path.isfile(tr_file)
obs_tr = pd.read_csv(tr_file, sep="\t", dtype=str)
assert obs_tr.columns.tolist() == expected_traceback.columns.tolist()
assert obs_tr.equals(expected_traceback)
def test_analysis():
"""Test traceback on a pure analysis run."""
# build fake run_dir
with tempfile.TemporaryDirectory() as tmpdir:
run_dir = Path(tmpdir, "example_dir")
step_dirs = [os.path.join(run_dir, "0_topoaa"),
os.path.join(run_dir, "1_caprieval")]
for d in [run_dir, *step_dirs]:
os.mkdir(d)
# run haddock3-traceback
main(run_dir)
# check traceback folder does not exist
assert not os.path.isdir(os.path.join(run_dir, "traceback"))
def test_get_steps_without_pdbs():
"""Test get_steps_without_pdbs."""
with tempfile.TemporaryDirectory() as tmpdir:
# build fake run_dir
run_dir = Path(tmpdir)
steps = ["0_topoaa", "1_rigidbody", "2_caprieval"]
for st in steps:
os.mkdir(Path(run_dir, st))
# create fake, empty pdb files
fake_pdb_path = Path(run_dir, steps[1] , f"rigidbody_1.pdb")
open(fake_pdb_path, "w").close()
# get steps without pdbs
obs_steps = get_steps_without_pdbs(run_dir, steps)
# check steps without pdbs
exp_steps = ["0_topoaa", "2_caprieval"]
assert obs_steps == exp_steps
# now we remove the fake pdb file
os.remove(fake_pdb_path)
# get steps without pdbs
obs_steps = get_steps_without_pdbs(run_dir, steps)
exp_steps = ["0_topoaa", "1_rigidbody", "2_caprieval"]
assert obs_steps == exp_steps
def test_subset_traceback(expected_traceback):
"""Test subset_traceback."""
with tempfile.TemporaryDirectory() as tmpdir:
cons_filename = Path(tmpdir, "consensus_example.tsv")
# subset traceback
obs_tr = subset_traceback(expected_traceback, cons_filename)
# assert consensus file exists
assert cons_filename.exists()
# check subset
exp_tr = [["Model", "1_rigidbody_rank", "4_flexref_rank", "Sum-of-Ranks"], # noqa: E501
["flexref_1.pdb", 1, 1, 2], # noqa: E501
["flexref_2.pdb", 2, 2, 4]] # noqa: E501
exp_tr_df = pd.DataFrame(exp_tr[1:], columns=exp_tr[0])
assert obs_tr.columns.tolist() == exp_tr_df.columns.tolist()
assert obs_tr.equals(exp_tr_df) |