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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 weblogo import seq_io
from weblogo.seq_io import genbank_io
from . import data_stream
def examples(): # type: ignore
return (
data_stream("genbank/NT_019265.gb"),
data_stream("genbank/cox2.gb"),
data_stream("genbank/iro.gb"),
data_stream("genbank/pri1.gb"),
data_stream("genbank/dbsource_wrap.gb"),
data_stream("genbank/noref.gb"),
data_stream("genbank/protein_refseq.gb"),
data_stream("genbank/cor6_6.gb"),
data_stream("genbank/origin_line.gb"),
# These files are too large to include in the distribution
# data_stream('genbank/arab1.gb'),
# data_stream('genbank/NC_005213.gbk'),
# data_stream('genbank/NC_003888.gbk'),
)
class test_genbank_io(unittest.TestCase):
# Useful for debugging
# def test_scan(self) :
# for f in examples():
# for t in genbank_io._scan(f):
# print t
# print
# print
def test_parse(self) -> None:
for f in examples():
# print f.name
genbank_io.read(f)
f.close()
# print seqs
def test_read(self) -> None:
f = data_stream("genbank/cox2.gb")
seqs = genbank_io.read(f)
self.assertEqual(len(seqs), 5)
self.assertEqual(len(seqs[1]), 210)
f.seek(0)
seqs = seq_io.read(f)
self.assertEqual(len(seqs), 5)
self.assertEqual(len(seqs[1]), 210)
f.close()
f = data_stream("genbank/NT_019265.gb")
seqs = genbank_io.read(f)
self.assertEqual(len(seqs), 0)
f.close()
if __name__ == "__main__":
unittest.main()
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