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# Copyright 2006-2014 by Peter Cock. All rights reserved.
# Revisions copyright 2011 Brandon Invergo. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for Bio.AlignIO.PhylipIO module."""
import unittest
from io import StringIO
from Bio.AlignIO.PhylipIO import PhylipIterator
from Bio.AlignIO.PhylipIO import PhylipWriter
class TestPhylipIO(unittest.TestCase):
def test_one(self):
input_file = "Phylip/one.dat"
with open(input_file) as handle:
ids = []
for alignment in PhylipIterator(handle):
for record in alignment:
ids.append(record.id)
self.assertEqual(
ids,
[
"V_Harveyi_",
"B_subtilis",
"B_subtilis",
"YA80_HAEIN",
"FLIY_ECOLI",
"E_coli_Gln",
"Deinococcu",
"HISJ_E_COL",
],
)
expected = (
"""mkklvlslsl vlafssataa faaipqniri gtdptyapfe sknsqgelvg
fdidlakelc krintqctfv enpldalips lkakkidaim sslsitekrq qeiaftdkly
aadsrlvvak nsdiqptves lkgkrvgvlq gttqetfgne hwapkgieiv syqgqdniys
dltagridaafqdevaaseg flkqpvgkdy kfggpsvkde klfgvgtgmg lrkednelre
alnkafaemradgtyeklak kyfdfdvygg""".replace(
" ", ""
)
.replace("\n", "")
.upper()
)
self.assertEqual(str(record.seq).replace("-", ""), expected)
def test_two_and_three(self):
path = "Phylip/two.dat"
# derived from http://atgc.lirmm.fr/phyml/usersguide.html
with open(path) as handle:
list2 = list(PhylipIterator(handle))
self.assertEqual(len(list2), 1)
self.assertEqual(len(list2[0]), 5)
path = "Phylip/three.dat"
with open(path) as handle:
list3 = list(PhylipIterator(handle))
self.assertEqual(len(list3), 1)
self.assertEqual(len(list3[0]), 5)
for i in range(5):
self.assertEqual(list2[0][i].id, list3[0][i].id)
self.assertEqual(list2[0][i].seq, list3[0][i].seq)
def test_four(self):
path = "Phylip/four.dat"
# File derived from here:
# http://evolution.genetics.washington.edu/phylip/doc/sequence.html
# Note the lack of any white space between names 2 and 3 and their seqs.
with open(path) as handle:
list4 = list(PhylipIterator(handle))
self.assertEqual(len(list4), 1)
self.assertEqual(len(list4[0]), 5)
def test_five(self):
# File derived rom here:
# http://evolution.genetics.washington.edu/phylip/doc/sequence.html
path = "Phylip/five.dat"
with open(path) as handle:
self.assertRaises(ValueError, list, PhylipIterator(handle))
def test_six(self):
# File derived rom here:
# http://evolution.genetics.washington.edu/phylip/doc/sequence.html
path = "Phylip/six.dat"
with open(path) as handle:
list5 = list(PhylipIterator(handle))
self.assertEqual(len(list5), 1)
def test_concatenation(self):
path = "Phylip/one.dat"
with open(path) as handle:
phylip_text = handle.read()
path = "Phylip/three.dat"
with open(path) as handle:
phylip_text3 = handle.read()
path = "Phylip/four.dat"
with open(path) as handle:
phylip_text4 = handle.read()
handle = StringIO(phylip_text4 + "\n" + phylip_text4)
self.assertEqual(len(list(PhylipIterator(handle))), 2)
handle = StringIO(phylip_text3 + "\n" + phylip_text4 + "\n\n\n" + phylip_text)
self.assertEqual(len(list(PhylipIterator(handle))), 3)
def test_write_read(self):
path = "Phylip/six.dat"
with open(path) as handle:
list5 = list(PhylipIterator(handle))
handle = StringIO()
PhylipWriter(handle).write_file(list5)
handle.seek(0)
list6 = list(PhylipIterator(handle))
self.assertEqual(len(list5), len(list6))
for a1, a2 in zip(list5, list6):
self.assertEqual(len(a1), len(a2))
for r1, r2 in zip(a1, a2):
self.assertEqual(r1.id, r2.id)
self.assertEqual(r1.seq, r2.seq)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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