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Move self-tests for Bio.PDB.PSEA to unit tests (#3980)

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Authored-by: Valentin Vareskic <valentin.vareskic@gmail.com>
This commit is contained in:
Valentin Vareskic
2022-07-26 18:08:32 +02:00
committed by GitHub
parent 257143be91
commit a8d2647a88
3 changed files with 127 additions and 13 deletions
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1
.gitignore vendored
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@ -125,3 +125,4 @@ Doc/api/*.rst
#Ignore virtual environment file
.env
venv/

13
Bio/PDB/PSEA.py
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@ -103,16 +103,3 @@ class PSEA:
def get_seq(self):
"""Return secondary structure string."""
return self.ss_seq
if __name__ == "__main__":
import sys
from Bio.PDB import PDBParser
# Parse PDB file
p = PDBParser()
s = p.get_structure("X", sys.argv[1])
# Annotate structure with PSEA secondary structure info
PSEA(s[0], sys.argv[1])

126
Tests/test_PDB_PSEA.py Normal file
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@ -0,0 +1,126 @@
# Copyright 2022 by Valentin Vareskic (valentin.vareskic@gmail.com).
# All rights reserved. This code is part of the Biopython distribution
# and governed by its license. Please see the LICENSE file that should
# have been included as part of this package.
"""Tests for PDB PSEA."""
import os
import unittest
from subprocess import getoutput
from Bio import MissingExternalDependencyError
from Bio.PDB import PDBParser
from Bio.PDB.PSEA import run_psea, psea, psea2HEC, PSEA
os.environ["LANG"] = "C"
cmd_output = getoutput("psea -h")
if not cmd_output.startswith("o---"):
raise MissingExternalDependencyError(
"Download and install psea from "
"ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. "
"Make sure that psea is on path"
)
def remove_sea_files():
for file in os.listdir():
if file.endswith(".sea"):
os.remove(file)
class TestPDBPSEA(unittest.TestCase):
def tearDown(self):
remove_sea_files()
def test_run_psea(self):
psae_run = run_psea("PDB/1A8O.pdb")
self.assertEqual(psae_run, "1A8O.sea")
def test_psea(self):
psae_run = psea("PDB/2BEG.pdb")
self.assertEqual(psae_run, "ccccbbbbbbbccccbbbbbbbbbbc")
def test_psea_2HEC(self):
seq = psea("PDB/2BEG.pdb")
psae_run = psea2HEC(seq)
self.assertEqual(
psae_run,
[
"C",
"C",
"C",
"C",
"E",
"E",
"E",
"E",
"E",
"E",
"E",
"C",
"C",
"C",
"C",
"E",
"E",
"E",
"E",
"E",
"E",
"E",
"E",
"E",
"E",
"C",
],
)
class TestPSEA(unittest.TestCase):
def tearDown(self):
remove_sea_files()
def test_get_seq(self):
p = PDBParser()
s = p.get_structure("X", "PDB/2BEG.pdb")
psea_class = PSEA(s[0], "PDB/2BEG.pdb")
self.assertEqual(
psea_class.get_seq(),
[
"C",
"C",
"C",
"C",
"E",
"E",
"E",
"E",
"E",
"E",
"E",
"C",
"C",
"C",
"C",
"E",
"E",
"E",
"E",
"E",
"E",
"E",
"E",
"E",
"E",
"C",
],
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)