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#!/usr/bin/env python
# Copyright (c) 2006, The Regents of the University of California, through
# Lawrence Berkeley National Laboratory (subject to receipt of any required
# approvals from the U.S. Dept. of Energy). All rights reserved.
# This software is distributed under the new BSD Open Source License.
# <http://www.opensource.org/licenses/bsd-license.html>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# (1) Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# (2) Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and or other materials provided with the distribution.
#
# (3) Neither the name of the University of California, Lawrence Berkeley
# National Laboratory, U.S. Dept. of Energy nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import unittest
from io import StringIO
from weblogo.seq import dna_alphabet, protein_alphabet
from weblogo.seq_io import clustal_io, nbrf_io, plain_io
from . import data_stream
class test_nbrf_io(unittest.TestCase):
def test_parse_cox2(self) -> None:
f = data_stream("cox2.nbrf")
seqs = nbrf_io.read(f)
self.assertEqual(len(seqs), 5)
self.assertEqual(len(seqs[1]), 210)
self.assertEqual(
str(seqs[0]),
"MAFILSFWMIFLLDSVIVLLSFVCFVCVWICALLFSTVLLVSKLNNIYCTWDFTASKFIDVYWFTIGGMFSLG"
"LLLRLCLLLYFGHLNFVSFDLCKVVGFQWYWVYFIFGETTIFSNLILESDYMIGDLRLLQCNHVLTLLSLVIY"
"KLWLSAVDVIHSFAISSLGVKVENLVAVMK",
)
self.assertEqual(seqs[0].alphabet, protein_alphabet)
f.close()
def test_parse_crab(self) -> None:
f = data_stream("crab.nbrf")
seqs = nbrf_io.read(f)
self.assertEqual(seqs[0].alphabet, protein_alphabet)
self.assertEqual(len(seqs), 9)
self.assertEqual(seqs[2].name, "CRAB_CHICK")
self.assertEqual(
seqs[2].description, "ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN)."
)
f.close()
def test_parse_dna(self) -> None:
f = data_stream("dna.pir")
seqs = nbrf_io.read(f)
self.assertEqual(seqs[0].alphabet, dna_alphabet)
self.assertEqual(len(seqs), 10)
f.close()
def test_parse_examples(self) -> None:
f = data_stream("rhod.pir")
seqs = nbrf_io.read(f)
self.assertEqual(seqs[0].alphabet, protein_alphabet)
self.assertEqual(len(seqs), 3)
f.close()
def test_parse_protein(self) -> None:
f = data_stream("protein.pir")
seqs = nbrf_io.read(f)
self.assertEqual(seqs[0].alphabet, protein_alphabet)
self.assertEqual(len(seqs), 10)
f.close()
def test_parse_clustal_fail(self) -> None:
# should fail with parse error
f = StringIO(clustal_io.example)
self.assertRaises(ValueError, nbrf_io.read, f, protein_alphabet)
def test_parse_plain_fail(self) -> None:
# should fail with parse error
f = StringIO(plain_io.example)
self.assertRaises(ValueError, nbrf_io.read, f)
def test_pir_file_from_clustal(self) -> None:
f = data_stream("clustalw.pir")
seqs = nbrf_io.read(f)
self.assertEqual(len(seqs), 2)
self.assertEqual(
seqs[1].endswith(
"C-AATC-G-CAATG-G--CTTGAACCGGGTAAAAGTCGT-A----------------------------------------"
"-----------------------------------------"
),
True,
)
f.close()
def test_parse_examples_alphabet(self) -> None:
f = data_stream("rhod.pir")
seqs = nbrf_io.read(f, alphabet=protein_alphabet)
self.assertEqual(seqs[0].alphabet, protein_alphabet)
self.assertEqual(len(seqs), 3)
f.close()
if __name__ == "__main__":
unittest.main()
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