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#!/usr/bin/env python
# Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
import unittest
from io import StringIO
from weblogo.seq import nucleic_alphabet, protein_alphabet
from weblogo.seq_io import clustal_io, fasta_io, table_io
from . import data_ref
class test_clustal_parser(unittest.TestCase):
def test_parse_clustal(self) -> None:
with data_ref("clustal.aln").open() as f:
seqs = clustal_io.read(f)
self.assertEqual(len(seqs), 7)
self.assertEqual(seqs[1].name, "CATH_HUMAN")
self.assertEqual(len(seqs[1]), 395)
def test_parse_clustal2_newline(self) -> None:
# Bug regression test. Clustal barfed on windows line endings, sometimes
with data_ref("clustalw2.aln").open() as f:
s = f.read()
import re
s = re.sub("\n", "\r\n", s) # Change to windows line endings
clustal_io.read(StringIO(s))
def test_parse_headerless(self) -> None:
with data_ref("clustal_headerless.aln").open() as f:
seqs = clustal_io.read(f)
self.assertEqual(len(seqs), 21)
self.assertEqual(seqs[2].name, "O16386_CAEEL")
self.assertEqual(len(seqs[1]), 137)
""" Wrong alphabet should throw a parsing error """
def test_parse_error(self) -> None:
with data_ref("clustal.aln").open() as f:
self.assertRaises(ValueError, clustal_io.read, f, nucleic_alphabet)
def test_parse_clustal181(self) -> None:
with data_ref("clustal181.aln").open() as f:
clustal_io.read(f)
def test_parse_clustal_glualign(self) -> None:
with data_ref("clustal_glualign.aln").open() as f:
clustal_io.read(f, nucleic_alphabet)
def test_parse_clustalw182(self) -> None:
with data_ref("clustalw182.aln").open() as f:
clustal_io.read(f, protein_alphabet)
def test_parse_fasta_fail(self) -> None:
# should fail with parse error
f = StringIO(fasta_io.example)
self.assertRaises(ValueError, clustal_io.read, f, protein_alphabet)
self.assertRaises(ValueError, clustal_io.read, f)
def test_parse_fasta_fail2(self) -> None:
# should fail with parse error
with data_ref("globin.fa").open() as f:
self.assertRaises(ValueError, clustal_io.read, f)
def test_parse_clustal_example(self) -> None:
f = StringIO(clustal_io.example)
clustal_io.read(f)
f.close()
def test_write(self) -> None:
f = StringIO(clustal_io.example)
seqs = clustal_io.read(f)
fout = StringIO()
clustal_io.write(fout, seqs)
fout.seek(0)
seqs2 = clustal_io.read(fout)
self.assertEqual(seqs, seqs2)
f.close()
def test_parse_table_fail(self) -> None:
# should fail with parse error
f = StringIO(table_io.example)
self.assertRaises(ValueError, clustal_io.read, f)
f.close()
def test_iterseq(self) -> None:
f = StringIO(clustal_io.example)
for s in clustal_io.iterseq(f):
pass
if __name__ == "__main__":
unittest.main()
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