#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 1118 João Pedro Rodrigues
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
Unit Tests for `pdb_shiftres`.
"""
import os
import sys
import unittest
from config import data_dir
from utils import OutputCapture
class TestTool(unittest.TestCase):
"""
Generic class for testing tools.
"""
def setUp(self):
# Dynamically import the module
name = 'pdbtools.pdb_shiftres'
self.module = __import__(name, fromlist=[''])
def exec_module(self):
"""
Execs module.
"""
with OutputCapture() as output:
try:
self.module.main()
except SystemExit as e:
self.retcode = e.code
self.stdout = output.stdout
self.stderr = output.stderr
return
def test_default(self):
"""$ pdb_shiftres data/dummy.pdb"""
# Simulate input
# pdb_shiftres dummy.pdb
sys.argv = ['', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
self.assertEqual(len(self.stdout), 204) # no lines deleted
self.assertEqual(len(self.stderr), 0) # no errors
records = (('ATOM', 'HETATM'))
resid_list = [int(l[22:26]) for l in self.stdout
if l.startswith(records)]
expected = [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, -1, -1, -1, -1, -1, -1, -1, -1, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
301, 302, 303, 301, 301, 302, 303, 304, 305]
self.assertEqual(resid_list, expected)
def test_single_option_1(self):
"""$ pdb_shiftres -10 data/dummy.pdb"""
# Simulate input
# pdb_shiftres dummy.pdb
sys.argv = ['', '-10', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
self.assertEqual(len(self.stdout), 204) # no lines deleted
self.assertEqual(len(self.stderr), 0) # no errors
records = (('ATOM', 'HETATM'))
resid_list = [int(l[22:26]) for l in self.stdout
if l.startswith(records)]
expected = [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 16, 16, 16, 16,
16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 11, 11, 11, 11,
11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12,
12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12,
12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12,
12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 9,
9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12,
12, 12, 12, 12, 12, 12, 12, 12, 12, 311, 312, 313, 311, 311,
312, 313, 314, 315]
self.assertEqual(resid_list, expected)
def test_single_option_2(self):
"""$ pdb_shiftres --10 data/dummy.pdb"""
# Simulate input
# pdb_shiftres dummy.pdb
sys.argv = ['', '--10', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
self.assertEqual(len(self.stdout), 204) # no lines deleted
self.assertEqual(len(self.stderr), 0) # no errors
records = (('ATOM', 'HETATM'))
resid_list = [int(l[22:26]) for l in self.stdout
if l.startswith(records)]
expected = [-6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6,
-6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -4, -4, -4, -4,
-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -3, -3, -3, -3,
-3, -3, -3, -3, -3, -3, -9, -9, -9, -9, -9, -9, -9, -9, -9,
-9, -9, -9, -9, -9, -9, -9, -9, -8, -8, -8, -8, -8, -8, -8,
-8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
-8, -8, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7,
-7, -7, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5,
-5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -8, -8,
-8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -11,
-11, -11, -11, -11, -11, -11, -11, -8, -8, -8, -8, -8, -8,
-8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, 291,
292, 293, 291, 291, 292, 293, 294, 295]
self.assertEqual(resid_list, expected)
def test_too_many_residues(self):
"""$ pdb_shiftres -9998 data/dummy.pdb"""
sys.argv = ['', '-9998', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(len(self.stderr), 1)
self.assertEqual(self.stderr[0][:22],
"Cannot set residue num") # proper error message
def test_file_not_found(self):
"""$ pdb_shiftres -10 not_existing.pdb"""
afile = os.path.join(data_dir, 'not_existing.pdb')
sys.argv = ['', '-10', afile]
self.exec_module()
self.assertEqual(self.retcode, 1) # exit code is 1 (error)
self.assertEqual(len(self.stdout), 0) # nothing written to stdout
self.assertEqual(self.stderr[0][:22],
"ERROR!! File not found") # proper error message
def test_file_missing(self):
"""$ pdb_shiftres -10"""
sys.argv = ['', '-10']
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0) # no output
self.assertEqual(self.stderr[0],
"ERROR!! No data to process!")
def test_helptext(self):
"""$ pdb_shiftres"""
sys.argv = ['']
self.exec_module()
self.assertEqual(self.retcode, 1) # ensure the program exited gracefully.
self.assertEqual(len(self.stdout), 0) # no output
self.assertEqual(self.stderr, self.module.__doc__.split("\n")[:-1])
def test_invalid_option(self):
"""$ pdb_shiftres -A data/dummy.pdb"""
sys.argv = ['', '-A', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0][:36],
"ERROR!! You provided an invalid numb")
def test_not_an_option(self):
"""$ pdb_shiftres 11 data/dummy.pdb"""
sys.argv = ['', '11', os.path.join(data_dir, 'dummy.pdb')]
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0],
"ERROR! First argument is not an option: '11'")
if __name__ == '__main__':
from config import test_dir
mpath = os.path.abspath(os.path.join(test_dir, '..'))
sys.path.insert(0, mpath) # so we load dev files before any installation
unittest.main()
