def test_concatenation(self):
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):
handle = StringIO(phylip_text5a)
list5 = list(PhylipIterator(handle))
handle.close()
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(str(r1.seq), str(r2.seq))
def test_two_and_three(self):
handle = StringIO(phylip_text2)
list2 = list(PhylipIterator(handle))
handle.close()
self.assertEqual(len(list2), 1)
self.assertEqual(len(list2[0]), 5)
handle = StringIO(phylip_text3)
list3 = list(PhylipIterator(handle))
handle.close()
self.assertEqual(len(list3), 1)
self.assertEqual(len(list3[0]), 5)
for i in range(0, 5):
self.assertEqual(list2[0][i].id, list3[0][i].id)
self.assertEqual(str(list2[0][i].seq), str(list3[0][i].seq))
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_one(self):
handle = StringIO(phylip_text)
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_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_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)
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(0, 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_a(self):
handle = StringIO(phylip_text5a)
list5 = list(PhylipIterator(handle))
handle.close()
self.assertEqual(len(list5), 1)
def test_five(self):
handle = StringIO(phylip_text5)
self.assertRaises(ValueError, list, PhylipIterator(handle))
handle.close()
def test_four(self):
handle = StringIO(phylip_text4)
list4 = list(PhylipIterator(handle))
handle.close()
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))