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# Copyright 2001 by Iddo Friedberg. 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 the FSSP module (DEPRECATED)."""
import os
import unittest
import warnings
from Bio import BiopythonDeprecationWarning
with warnings.catch_warnings():
warnings.simplefilter("ignore", BiopythonDeprecationWarning)
# modules to be tested
from Bio import FSSP
from Bio.FSSP import FSSPTools
class TestGeo(unittest.TestCase):
@classmethod
def setUpClass(cls):
path = os.path.join("FSSP", "1cnv.fssp")
with open(path) as handle:
cls.head_rec, cls.sum_rec, cls.align_rec = FSSP.read_fssp(handle)
def test_attributes(self):
self.assertEqual(self.head_rec.author, ["M.Hennig"])
self.assertEqual(self.head_rec.compnd, ["concanavalin", "b"])
self.assertEqual(self.head_rec.database, 2645)
self.assertEqual(self.head_rec.header, "SEED PROTEIN")
self.assertEqual(self.head_rec.nalign, 214)
self.assertEqual(self.head_rec.pdbid, "1cnv")
self.assertEqual(self.head_rec.seqlength, 283)
self.assertEqual(self.head_rec.source, "(canavalia ensiformis) jack bean")
def test_alignment(self):
self.assertEqual(len(self.sum_rec), self.head_rec.nalign)
alignment = FSSPTools.mult_align(self.sum_rec, self.align_rec)
name_list = ["2hvm0", "1hvq0", "1nar0", "2ebn0"]
sum_newnames, align_newnames = FSSPTools.name_filter(
self.sum_rec, self.align_rec, name_list
)
self.assertEqual(len(sum_newnames), 4)
line = """\
2: 1cnv 2hvm 39.2 1.7 270 273 42 0 0 10 S hevamine (chitinaseLYSOZYME)
""" # noqa : W291
self.assertEqual(str(sum_newnames[2]), line)
line = """\
3: 1cnv 1hvq 39.0 1.7 271 273 41 0 0 10 S hevamine a
""" # noqa : W291
self.assertEqual(str(sum_newnames[3]), line)
line = """\
5: 1cnv 1nar 20.0 3.1 246 289 13 0 0 27 S Narbonin
""" # noqa : W291
self.assertEqual(str(sum_newnames[5]), line)
line = """\
11: 1cnv 2ebn 16.9 3.0 215 285 13 0 0 25 S Endo-beta-n-acetylglucosaminidase f1 (endoglycosidase f
""" # noqa : W291
self.assertEqual(str(sum_newnames[11]), line)
new_dict = align_newnames["0P168"].pos_align_dict
self.assertEqual(len(new_dict), 4)
self.assertEqual(str(new_dict[2]), "Ps")
self.assertEqual(str(new_dict[3]), "Ps")
self.assertEqual(str(new_dict[5]), "..")
self.assertEqual(str(new_dict[11]), "..")
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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