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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, plain_io
from . import data_stream
example_with_optional_comments = """
>SEQUENCE_1
;comment line 1 (optional)
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
>SEQUENCE_2
;comment line 1 (optional)
;comment line 2 (optional)
SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH
"""
example3 = """
>
AAAGTG
>
AAAGCG
>
TGCCCT
>
TGCCTT
"""
example4 = """
>
AAAGTG
>
AAAGCG
TGCCCT
>
TGCCTT
"""
class test_fasta_io(unittest.TestCase):
def test_read(self) -> None:
f = StringIO(fasta_io.example)
seqs = fasta_io.read(f)
# print seqs
self.assertEqual(len(seqs), 3)
self.assertEqual(seqs[0].description, "Lamprey GLOBIN V - SEA LAMPREY")
self.assertEqual(seqs[0].name, "Lamprey")
self.assertEqual(len(seqs[1]), 231)
# def test_read_long(self) -> None:
# f = data_stream("NC_000913.ffn")
# count = 0
# start = time.time()
# for s in seq_io.fasta_io.read_seq(f):
# count +=1
# end = time.time()
# t = end-start
#
# self.assertEqual(count, 4243)
#
# # Timing is 3s 1.67 GHz G4
# # print t
def test_read_fail(self) -> None:
f = StringIO(fasta_io.example)
# Wrong alphabet
self.assertRaises(ValueError, fasta_io.read, f, nucleic_alphabet)
def test_parse_globin(self) -> None:
# f = open_resource(__file__, "test_data", "globin.fa")
f = data_stream("globin.fa")
seqs = fasta_io.read(f, protein_alphabet)
self.assertEqual(len(seqs), 56)
f.close()
def test_parse_clustal_fail(self) -> None:
# should fail with parse error
f = StringIO(clustal_io.example)
self.assertRaises(ValueError, fasta_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, fasta_io.read, f)
def test_write_seq(self) -> None:
f = StringIO(fasta_io.example)
seqs = fasta_io.read(f)
fout = StringIO()
fasta_io.write(fout, seqs)
fout.seek(0)
seqs2 = fasta_io.read(fout)
self.assertEqual(seqs, seqs2)
def test_write_with_header(self) -> None:
f = StringIO(fasta_io.example)
seqs = fasta_io.read(f)
seqs.description = "A description\nMore description"
fout = StringIO()
fasta_io.write(fout, seqs)
def test_read_comments(self) -> None:
f = StringIO(example_with_optional_comments)
seqs = fasta_io.read(f)
self.assertEqual(len(seqs), 2)
self.assertEqual(seqs[1].startswith("SATVSEI"), True)
self.assertEqual(
seqs[1].description.splitlines()[1], ("comment line 1 (optional)")
)
def test_write_comments(self) -> None:
f = StringIO(example_with_optional_comments)
seqs = fasta_io.read(f)
fout = StringIO()
fasta_io.write(fout, seqs)
fout.seek(0)
seqs2 = fasta_io.read(fout)
self.assertEqual(seqs, seqs2)
self.assertEqual(seqs[1].description, seqs2[1].description)
def test_read_headerless(self) -> None:
# This example has blank headers.
f = StringIO(example3)
seqs = fasta_io.read(f)
self.assertEqual(len(seqs), 4)
# print seqs
fout = StringIO()
fasta_io.write(fout, seqs)
def test_read_empty(self) -> None:
f = StringIO()
seqs = fasta_io.read(f)
assert len(seqs) == 0
def test_isaligned(self) -> None:
seqs = fasta_io.read(StringIO())
assert seqs.isaligned()
seqs = fasta_io.read(StringIO(fasta_io.example))
assert seqs.isaligned()
seqs = fasta_io.read(StringIO(example4))
assert not seqs.isaligned()
def test_read_with_blank_line(self) -> None:
f = StringIO(example4)
seqs = fasta_io.read(f)
assert not seqs.isaligned()
self.assertEqual(len(seqs), 3)
if __name__ == "__main__":
unittest.main()
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