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from benchmark import get_cath
import numpy as np
from pathlib import Path
import os
import sys
location=Path(__file__).parent.resolve()
PATH_TO_PDB=Path(sys.argv[1])
assert (PATH_TO_PDB.exists()), 'PDB directory is missing!'
def test_load_CATH():
"""Tests basic benchmark functions - loading data, calculating metrics, ect."""
cath_location = location.parents[0]/"cath-domain-description-file.txt"
cath_df = get_cath.read_data(cath_location)
new_df=get_cath.filter_with_user_list(cath_df,location/'test_set.txt')
# check shape
assert new_df.shape == (10, 8), "DataFrame shape is incorrect"
pdbs = get_cath.get_pdbs(new_df,1,20)
assert pdbs.shape == (1, 8), "Filtered shape is incorrect"
# check sequence, 1a41A02 fragment.
new_df = get_cath.append_sequence(new_df,PATH_TO_PDB)
fragment_sequence=new_df[new_df.PDB == "1a41"]
sequence=fragment_sequence.sequence.values[0]
start=fragment_sequence.start.values[0]
stop=fragment_sequence.stop.values[0]
assert (sequence[start:stop+1] == "IRIKDLRTYGVNYTFLYNFWTNVKSISPLPSPKKLIALTIKQTAEVVGHTPSISKRAYMATTILEMVKDKNFLDVVSKTTFDEFLSIVVDHVKS"
), "Sequence assigned incorrectly"
#check sequence, 1cruA00 fragment
fragment_sequence=new_df[new_df.PDB == "1cru"]
sequence=fragment_sequence.sequence.values[0]
start=fragment_sequence.start.values[0]
stop=fragment_sequence.stop.values[0]
assert (sequence[start:stop+1] == "DVPLTPSQFAKAKSENFDKKVILSNLNKPHALLWGPDNQIWLTERATGKILRVNPESGSVKTVFQVPEIVNDADGQNGLLGFAFHPDFKNNPYIYISGTFKNPKSKELPNQTIIRRYTYNKSTDTLEKPVDLLAGLPSSKDHQSGRLVIGPDQKIYYTIGDQGRNQLAYLFLPNQAQHTPTQQELNGKDYHTYMGKVLRLNLDGSIPKDNPSFNGVVSHIYTLGHRNPQGLAFTPNGKLLQSEQGPNSDDEINLIVKGGNYGWPNVAGYKDDSGYAYANYSAAANKSIKDLAQNGVKVAAGVPVTKESEWTGKNFVPPLKTLYTVQDTYNYNDPTCGEMTYICWPTVAPSSAYVYKGGKKAITGWENTLLVPSLKRGVIFRIKLDPTYSTTYDDAVPMFKSNNRYRDVIASPDGNVLYVLTDTAGNVQKDDGSVTNTLENPGSLIKFT"
), "Sequence assigned incorrectly"
#load predictions
path_to_file=Path(location/'test_data.csv')
with open(path_to_file.with_suffix('.txt')) as datasetmap:
predictions = get_cath.load_prediction_matrix(new_df, path_to_file.with_suffix('.txt'), path_to_file)
# check accuracy and recall
accuracy,recall=get_cath.score_each(new_df,predictions,by_fragment=True)
assert (
abs(accuracy[0] - 0.298) <= 0.001
), "Sequence recovery calculated incorrectly"
accuracy,recall=get_cath.score_each(new_df,predictions,by_fragment=True)
assert (
abs(recall[3] - 0.384) <= 0.001
), "Macro-recall calculated incorrectly"
def test_command_line():
"""Tests command line interface"""
os.system(f'python {location.parents[0]/"run_benchmark.py"} --dataset {location/"test_set.txt"} --path_to_pdb {PATH_TO_PDB} --path_to_models {location} --training_set {location/"trainingset.txt"}')
assert (Path(location/'test_data.csv.pdf').exists()), 'Failed to produce plots!'
assert (Path(location/'test_data_1a41.pdb').exists()), 'Failed to produce PDB with accuracy and entropy!'
if __name__=='__main__':
test_load_CATH()
test_command_line()
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