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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 import seq_io
from weblogo.seq import nucleic_alphabet, protein_alphabet
from weblogo.seq_io import (
array_io,
clustal_io,
fasta_io,
genbank_io,
msf_io,
nbrf_io,
nexus_io,
phylip_io,
plain_io,
stockholm_io,
table_io,
)
from . import data_stream, test_genbank_io
class test_seq_io(unittest.TestCase):
def test_attr(self) -> None:
f = seq_io.formats
for i in f:
i.names[0] # Ensure every format has a name.
seq_io.format_names()
seq_io.format_extensions()
def test_parse_clustal(self) -> None:
with data_stream("clustal.aln") as f:
seqs = seq_io.read(f)
self.assertEqual(len(seqs), 7)
self.assertEqual(seqs[1].name, "CATH_HUMAN")
self.assertEqual(len(seqs[1]), 395)
def test_parse_error(self) -> None:
"""Wrong alphabet should throw a parsing error"""
with data_stream("clustal.aln") as f:
self.assertRaises(ValueError, seq_io.read, f, nucleic_alphabet)
def test_parse_clustal181(self) -> None:
with data_stream("clustal181.aln") as f:
seq_io.read(f, protein_alphabet)
def test_parse_clustal_glualign(self) -> None:
with data_stream("clustal_glualign.aln") as f:
seq_io.read(f, nucleic_alphabet)
def test_parse_clustalw182(self) -> None:
with data_stream("clustalw182.aln") as f:
seq_io.read(f, protein_alphabet)
def test_read_example_array(self) -> None:
f = StringIO(array_io.example)
seqs = seq_io.read(f)
# print seqs
self.assertEqual(len(seqs), 8)
self.assertEqual(seqs[0].name, "")
self.assertEqual(len(seqs[1]), 60)
def test_read_fasta(self) -> None:
f = StringIO(fasta_io.example)
seqs = seq_io.read(f)
# print seqs
self.assertEqual(len(seqs), 3)
self.assertEqual(seqs[0].description, "Lamprey GLOBIN V - SEA LAMPREY")
self.assertEqual(len(seqs[1]), 231)
def test_parse_globin_fasta(self) -> None:
with data_stream("globin.fa") as f:
seqs = seq_io.read(f)
self.assertEqual(len(seqs), 56)
def test_parser_extensions(self) -> None:
# Test that the list of extension is a list.
# Very easy with one extension list to write ('txt') rather than ('txt',)
for p in seq_io._parsers:
self.assertTrue(type(p.extensions) is tuple)
def test_parser_names(self) -> None:
# Same for names
for p in seq_io._parsers:
self.assertTrue(type(p.names) is tuple)
def test_parsers(self) -> None:
# seq_io._parsers is an ordered list of sequence parsers that are
# tried, in turn, on files of unknown format. Each parser must raise
# an exception when fed a format further down the list.
# We may include examples here for parsers that are not currently in
# seq_io._parsers
# TODO: Refactor these examples as with test_genbank_io.examples()
# TODO: Then test that each example works with read() and iterseq()
# TODO: Also autotest Write and writeseq, where available.
fasta_examples = (StringIO(fasta_io.example), data_stream("globin.fa"))
clustal_examples = (
StringIO(clustal_io.example),
data_stream("clustal.aln"),
data_stream("clustal181.aln"),
data_stream("clustal_glualign.aln"),
data_stream("clustalw182.aln"),
)
plain_examples = (StringIO(plain_io.example),)
phylip_examples = (
data_stream("phylip_test_1.phy"),
data_stream("phylip_test_2.phy"),
data_stream("phylip_test_3.phy"),
data_stream("phylip_test_4.phy"),
data_stream("phylip_test_5.phy"),
data_stream("dna.phy"),
)
msf_examples = (
data_stream("dna.msf"),
data_stream("cox2.msf"),
data_stream("1beo.msf"),
)
nbrf_examples = (
data_stream("cox2.nbrf"),
data_stream("crab.nbrf"),
data_stream("dna.pir"),
data_stream("rhod.pir"),
data_stream("protein.pir"),
)
nexus_examples = (
data_stream("nexus/protein.nex"),
data_stream("nexus/dna.nex"),
)
stockholm_examples = (
StringIO(stockholm_io.example),
data_stream("pfam_example.txt"),
data_stream("pfam.txt"),
)
table_examples = (StringIO(table_io.example),)
array_examples = (StringIO(array_io.example),)
examples = {
fasta_io: fasta_examples,
clustal_io: clustal_examples,
plain_io: plain_examples,
phylip_io: phylip_examples,
msf_io: msf_examples,
nbrf_io: nbrf_examples,
nexus_io: nexus_examples,
stockholm_io: stockholm_examples,
table_io: table_examples,
array_io: array_examples,
genbank_io: test_genbank_io.examples(),
}
parsers = seq_io._parsers
for i in range(0, len(parsers)):
for j in range(i + 1, len(parsers)):
# Check that parser[i] cannot read files intended for parser[j] (where j>i)
for f in examples[parsers[j]]:
# print parsers[i].names[0], parsers[j].names[0]
f.seek(0)
self.assertRaises(ValueError, parsers[i].read, f)
# When fed an empty file, the parser should either raise a ValueError
# or return an empty SeqList
e = StringIO()
for p in seq_io._parsers:
try:
s = p.read(e)
self.assertEqual(len(s), 0)
except ValueError:
pass
for e in examples.values():
for f in e:
f.close()
if __name__ == "__main__":
unittest.main()
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