def check_reading_writing(self, path):
alignments = AlignmentIterator(path)
stream = StringIO()
writer = AlignmentWriter(stream)
n = writer.write_file(alignments, mincount=1, maxcount=1)
self.assertEqual(n, 1)
alignments = AlignmentIterator(path)
alignment = next(alignments)
stream.seek(0)
saved_alignments = AlignmentIterator(stream)
saved_alignment = next(saved_alignments)
with self.assertRaises(StopIteration):
next(saved_alignments)
self.assertEqual(len(alignment), len(saved_alignment))
for i, (sequence, saved_sequence) in enumerate(
zip(alignment.sequences, saved_alignment.sequences)):
self.assertEqual(sequence.id, saved_sequence.id)
self.assertEqual(sequence.seq, saved_sequence.seq)
self.assertEqual(alignment[i], saved_alignment[i])
self.assertTrue(
numpy.array_equal(alignment.coordinates,
saved_alignment.coordinates))
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 stream:
alignments = AlignmentIterator(stream)
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.assertEqual(
repr(alignment),
"<Bio.Align.Alignment object (5 rows x 42 columns) at 0x%x>"
% id(alignment),
)
self.assertEqual(len(alignment), 5)
self.assertEqual(alignment.sequences[0].id, "Turkey")
self.assertEqual(alignment.sequences[1].id, "Salmo gair")
self.assertEqual(alignment.sequences[2].id, "H. Sapiens")
self.assertEqual(alignment.sequences[3].id, "Chimp")
self.assertEqual(alignment.sequences[4].id, "Gorilla")
self.assertEqual(
alignment.sequences[0].seq, "AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT"
)
self.assertEqual(
alignment.sequences[1].seq, "AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT"
)
self.assertEqual(
alignment.sequences[2].seq, "ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA"
)
self.assertEqual(
alignment.sequences[3].seq, "AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT"
)
self.assertEqual(
alignment.sequences[4].seq, "AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA"
)
self.assertEqual(alignment[0], "AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT")
self.assertEqual(alignment[1], "AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT")
self.assertEqual(alignment[2], "ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA")
self.assertEqual(alignment[3], "AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT")
self.assertEqual(alignment[4], "AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA")
self.check_reading_writing(path)
self.assertTrue(
numpy.array_equal(
alignment.coordinates,
numpy.array([[0, 42], [0, 42], [0, 42], [0, 42], [0, 42]]),
)
)
def test_five_and_six(self):
paths = ("Phylip/five.dat", "Phylip/six.dat")
# http://evolution.genetics.washington.edu/phylip/doc/sequence.html
for path in paths:
with open(path) as stream:
alignments = AlignmentIterator(stream)
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.assertEqual(
repr(alignment),
"<Bio.Align.Alignment object (5 rows x 42 columns) at 0x%x>"
% id(alignment),
)
self.assertEqual(len(alignment), 5)
self.assertEqual(alignment.sequences[0].id, "Turkey")
self.assertEqual(alignment.sequences[1].id, "Salmo gair")
self.assertEqual(alignment.sequences[2].id, "H. Sapiens")
self.assertEqual(alignment.sequences[3].id, "Chimp")
self.assertEqual(alignment.sequences[4].id, "Gorilla")
self.assertEqual(
alignment.sequences[0].seq, "AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT"
)
self.assertEqual(
alignment.sequences[1].seq, "AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT"
)
self.assertEqual(
alignment.sequences[2].seq, "ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA"
)
self.assertEqual(
alignment.sequences[3].seq, "AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT"
)
self.assertEqual(
alignment.sequences[4].seq, "AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA"
)
self.assertEqual(alignment[0], "AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT")
self.assertEqual(alignment[1], "AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT")
self.assertEqual(alignment[2], "ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA")
self.assertEqual(alignment[3], "AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT")
self.assertEqual(alignment[4], "AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA")
self.assertTrue(
numpy.array_equal(
alignment.coordinates,
numpy.array([[0, 42], [0, 42], [0, 42], [0, 42], [0, 42]]),
)
)
self.check_reading_writing(path)
def test_one(self):
path = "Phylip/one.dat"
with open(path) as stream:
alignments = AlignmentIterator(stream)
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.assertEqual(
repr(alignment),
"<Bio.Align.Alignment object (8 rows x 286 columns) at 0x%x>"
% id(alignment),
)
self.assertEqual(len(alignment), 8)
self.assertEqual(alignment.sequences[0].id, "V_Harveyi_")
self.assertEqual(alignment.sequences[1].id, "B_subtilis")
self.assertEqual(alignment.sequences[2].id, "B_subtilis")
self.assertEqual(alignment.sequences[3].id, "YA80_HAEIN")
self.assertEqual(alignment.sequences[4].id, "FLIY_ECOLI")
self.assertEqual(alignment.sequences[5].id, "E_coli_Gln")
self.assertEqual(alignment.sequences[6].id, "Deinococcu")
self.assertEqual(alignment.sequences[7].id, "HISJ_E_COL")
self.assertEqual(
alignment.sequences[0].seq,
"MKNWIKVAVAAIALSAATVQAATEVKVGMSGRYFPFTFVKQDKLQGFEVDMWDEIGKRNDYKIEYVTANFSGLFGLLETGRIDTISNQITMTDARKAKYLFADPYVVDGAQITVRKGNDSIQGVEDLAGKTVAVNLGSNFEQLLRDYDKDGKINIKTYDTGIEHDVALGRADAFIMDRLSALELIKKTGLPLQLAGEPFETIQNAWPFVDNEKGRKLQAEVNKALAEMRADGTVEKISVKWFGADITK",
)
self.assertEqual(
alignment.sequences[1].seq,
"MKMKKWTVLVVAALLAVLSACGNGNSSSKEDDNVLHVGATGQSYPFAYKENGKLTGFDVEVMEAVAKKIDMKLDWKLLEFSGLMGELQTGKLDTISNQVAVTDERKETYNFTKPYAYAGTQIVVKKDNTDIKSVDDLKGKTVAAVLGSNHAKNLESKDPDKKINIKTYETQEGTLKDVAYGRVDAYVNSRTVLIAQIKKTGLPLKLAGDPIVYEQVAFPFAKDDAHDKLRKKVNKALDELRKDGTLKKLSEKYFNEDITVEQKH",
)
self.assertEqual(
alignment.sequences[2].seq,
"MKKALLALFMVVSIAALAACGAGNDNQSKDNAKDGDLWASIKKKGVLTVGTEGTYEPFTYHDKDTDKLTGYDVEVITEVAKRLGLKVDFKETQWGSMFAGLNSKRFDVVANQVGKTDREDKYDFSDKYTTSRAVVVTKKDNNDIKSEADVKGKTSAQSLTSNYNKLATNAGAKVEGVEGMAQALQMIQQARVDMTYNDKLAVLNYLKTSGNKNVKIAFETGEPQSTYFTFRKGSGEVVDQVNKALKEMKEDGTLSKISKKWFGEDVSK",
)
self.assertEqual(
alignment.sequences[3].seq,
"MKKLLFTTALLTGAIAFSTFSHAGEIADRVEKTKTLLVGTEGTYAPFTFHDKSGKLTGFDVEVIRKVAEKLGLKVEFKETQWDAMYAGLNAKRFDVIANQTNPSPERLKKYSFTTPYNYSGGVIVTKSSDNSIKSFEDLKGRKSAQSATSNWGKDAKAAGAQILVVDGLAQSLELIKQGRAEATINDKLAVLDYFKQHPNSGLKIAYDRGDKTPTAFAFLQGEDALITKFNQVLEALRQDGTLKQISIEWFGYDITQ",
)
self.assertEqual(
alignment.sequences[4].seq,
"MKLAHLGRQALMGVMAVALVAGMSVKSFADEGLLNKVKERGTLLVGLEGTYPPFSFQGDDGKLTGFEVEFAQQLAKHLGVEASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTISGIQALVKKGNEGTIKTADDLKGKKVGVGLGTNYEEWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALDLVKKTNDTLAVTGEAFSRQESGVALRKGNEDLLKAVNDAIAEMQKDGTLQALSEKWFGADVTK",
)
self.assertEqual(
alignment.sequences[5].seq,
"MKSVLKVSLAALTLAFAVSSHAADKKLVVATDTAFVPFEFKQGDKYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTEPK",
)
self.assertEqual(
alignment.sequences[6].seq,
"MKKSLLSLKLSGLLVPSVLALSLSACSSPSSTLNQGTLKIAMEGTYPPFTSKNEQGELVGFDVDIAKAVAQKLNLKPEFVLTEWSGILAGLQANKYDVIVNQVGITPERQNSIGFSQPYAYSRPEIIVAKNNTFNPQSLADLKGKRVGSTLGSNYEKQLIDTGDIKIVTYPGAPEILADLVAGRIDAAYNDRLVVNYIINDQKLPVRGAGQIGDAAPVGIALKKGNSALKDQIDKALTEMRSDGTFEKISQKWFGQDVGQP",
)
self.assertEqual(
alignment.sequences[7].seq,
"MKKLVLSLSLVLAFSSATAAFAAIPQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMRADGTYEKLAKKYFDFDVYGG",
)
self.assertEqual(
alignment[0],
"--MKNWIKVAVAAIA--LSAA------------------TVQAATEVKVGMSGRYFPFTFVKQ--DKLQGFEVDMWDEIGKRNDYKIEYVTANFSGLFGLLETGRIDTISNQITMTDARKAKYLFADPYVVDG-AQITVRKGNDSIQGVEDLAGKTVAVNLGSNFEQLLRDYDKDGKINIKTYDT--GIEHDVALGRADAFIMDRLSALE-LIKKT-GLPLQLAGEPFETI-----QNAWPFVDNEKGRKLQAEVNKALAEMRADGTVEKISVKWFGADITK----",
)
self.assertEqual(
alignment[1],
"MKMKKWTVLVVAALLAVLSACG------------NGNSSSKEDDNVLHVGATGQSYPFAYKEN--GKLTGFDVEVMEAVAKKIDMKLDWKLLEFSGLMGELQTGKLDTISNQVAVTDERKETYNFTKPYAYAG-TQIVVKKDNTDIKSVDDLKGKTVAAVLGSNHAKNLESKDPDKKINIKTYETQEGTLKDVAYGRVDAYVNSRTVLIA-QIKKT-GLPLKLAGDPIVYE-----QVAFPFAKDDAHDKLRKKVNKALDELRKDGTLKKLSEKYFNEDITVEQKH",
)
self.assertEqual(
alignment[2],
"MKKALLALFMVVSIAALAACGAGNDNQSKDNAKDGDLWASIKKKGVLTVGTEGTYEPFTYHDKDTDKLTGYDVEVITEVAKRLGLKVDFKETQWGSMFAGLNSKRFDVVANQVG-KTDREDKYDFSDKYTTSR-AVVVTKKDNNDIKSEADVKGKTSAQSLTSNYNKLATN----AGAKVEGVEGMAQALQMIQQARVDMTYNDKLAVLN-YLKTSGNKNVKIAFETGEPQ-----STYFTFRKGS--GEVVDQVNKALKEMKEDGTLSKISKKWFGEDVSK----",
)
self.assertEqual(
alignment[3],
"MKKLLFTTALLTGAIAFSTF-----------SHAGEIADRVEKTKTLLVGTEGTYAPFTFHDK-SGKLTGFDVEVIRKVAEKLGLKVEFKETQWDAMYAGLNAKRFDVIANQTNPSPERLKKYSFTTPYNYSG-GVIVTKSSDNSIKSFEDLKGRKSAQSATSNWGKDAKA----AGAQILVVDGLAQSLELIKQGRAEATINDKLAVLD-YFKQHPNSGLKIAYDRGDKT-----PTAFAFLQGE--DALITKFNQVLEALRQDGTLKQISIEWFGYDITQ----",
)
self.assertEqual(
alignment[4],
"MKLAHLGRQALMGVMAVALVAG---MSVKSFADEG-LLNKVKERGTLLVGLEGTYPPFSFQGD-DGKLTGFEVEFAQQLAKHLGVEASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTISGIQALVKKGNEGTIKTADDLKGKKVGVGLGTNYEEWLRQNV--QGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALD-LVKKT-NDTLAVTGEAFSRQ-----ESGVALRKGN--EDLLKAVNDAIAEMQKDGTLQALSEKWFGADVTK----",
)
self.assertEqual(
alignment[5],
"--MKSVLKVSLAALTLAFAVS------------------SHAADKKLVVATDTAFVPFEFKQG--DKYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSG-LLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKAN--IKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILY-FIKTAGNGQFKAVGDSLEAQ-----QYGIAFPKGS--DELRDKVNGALKTLRENGTYNEIYKKWFGTEPK-----",
)
self.assertEqual(
alignment[6],
"-MKKSLLSLKLSGLLVPSVLALS--------LSACSSPSSTLNQGTLKIAMEGTYPPFTSKNE-QGELVGFDVDIAKAVAQKLNLKPEFVLTEWSGILAGLQANKYDVIVNQVGITPERQNSIGFSQPYAYSRPEIIVAKNNTFNPQSLADLKGKRVGSTLGSNYEKQLIDTG---DIKIVTYPGAPEILADLVAGRIDAAYNDRLVVNY-IINDQ-KLPVRGAGQIGDAA-----PVGIALKKGN--SALKDQIDKALTEMRSDGTFEKISQKWFGQDVGQP---",
)
self.assertEqual(
alignment[7],
"MKKLVLSLSLVLAFSSATAAF-------------------AAIPQNIRIGTDPTYAPFESKNS-QGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQP-TVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKED--NELREALNKAFAEMRADGTYEKLAKKYFDFDVYGG---",
)
self.assertTrue(
numpy.array_equal(
alignment.coordinates,
numpy.array(
[
[
0,
0,
0,
13,
13,
16,
17,
17,
17,
17,
17,
17,
17,
17,
17,
18,
41,
41,
41,
90,
91,
109,
109,
121,
122,
146,
147,
148,
149,
150,
151,
160,
160,
183,
183,
188,
188,
202,
202,
212,
214,
247,
248,
248,
248,
],
[
0,
1,
2,
15,
17,
20,
21,
22,
22,
22,
22,
22,
23,
24,
27,
28,
51,
51,
51,
100,
101,
119,
119,
131,
132,
156,
157,
158,
159,
160,
161,
170,
172,
195,
195,
200,
200,
214,
214,
224,
226,
259,
260,
261,
264,
],
[
0,
1,
2,
15,
17,
20,
21,
22,
23,
25,
31,
34,
35,
36,
39,
40,
63,
64,
65,
114,
114,
132,
132,
144,
145,
169,
169,
169,
169,
169,
170,
179,
181,
204,
204,
209,
210,
224,
224,
234,
234,
267,
268,
268,
268,
],
[
0,
1,
2,
15,
17,
20,
20,
20,
20,
20,
20,
23,
24,
25,
28,
29,
52,
52,
53,
102,
103,
121,
121,
133,
134,
158,
158,
158,
158,
158,
159,
168,
170,
193,
193,
198,
199,
213,
213,
223,
223,
256,
257,
257,
257,
],
[
0,
1,
2,
15,
17,
20,
21,
22,
22,
22,
28,
31,
32,
32,
35,
36,
59,
59,
60,
109,
110,
128,
129,
141,
142,
166,
167,
168,
168,
168,
169,
178,
180,
203,
203,
208,
208,
222,
222,
232,
232,
265,
266,
266,
266,
],
[
0,
0,
0,
13,
15,
18,
19,
19,
19,
19,
19,
19,
19,
19,
19,
20,
43,
43,
43,
92,
93,
111,
111,
123,
124,
148,
149,
149,
149,
150,
151,
160,
162,
185,
185,
190,
191,
205,
205,
215,
215,
248,
248,
248,
248,
],
[
0,
0,
1,
14,
16,
19,
20,
21,
22,
22,
22,
25,
26,
27,
30,
31,
54,
54,
55,
104,
105,
123,
124,
136,
137,
161,
162,
163,
163,
163,
163,
172,
174,
197,
197,
202,
202,
216,
216,
226,
226,
259,
260,
261,
261,
],
[
0,
1,
2,
15,
17,
20,
21,
21,
21,
21,
21,
21,
21,
21,
21,
21,
44,
44,
45,
94,
95,
113,
114,
126,
126,
150,
151,
152,
153,
154,
155,
164,
166,
189,
190,
195,
196,
210,
215,
225,
225,
258,
259,
260,
260,
],
]
),
)
)
self.check_reading_writing(path)
def test_two_and_three(self):
paths = ("Phylip/two.dat", "Phylip/three.dat")
# derived from http://atgc.lirmm.fr/phyml/usersguide.html
for path in paths:
with open(path) as stream:
alignments = AlignmentIterator(stream)
alignment = next(alignments)
with self.assertRaises(StopIteration):
next(alignments)
self.assertEqual(
repr(alignment),
"<Bio.Align.Alignment object (5 rows x 60 columns) at 0x%x>"
% id(alignment),
)
self.assertEqual(len(alignment), 5)
self.assertEqual(alignment.sequences[0].id, "Tax1")
self.assertEqual(alignment.sequences[1].id, "Tax2")
self.assertEqual(alignment.sequences[2].id, "Tax3")
self.assertEqual(alignment.sequences[3].id, "Tax4")
self.assertEqual(alignment.sequences[4].id, "Tax5")
self.assertEqual(
alignment.sequences[0].seq,
"CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAGGAAATGGTCAATATTACAAGGT",
)
self.assertEqual(
alignment.sequences[1].seq,
"CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAACATTAAAAGAT",
)
self.assertEqual(
alignment.sequences[2].seq,
"CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGGGAAATCGTCAATATTAAAAGGT",
)
self.assertEqual(
alignment.sequences[3].seq,
"TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGGGAAATGGTCAATCTTAAAAGGT",
)
self.assertEqual(
alignment.sequences[4].seq,
"CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAATATTAAAAGGT",
)
self.assertEqual(
alignment[0],
"CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAGGAAATGGTCAATATTACAAGGT",
)
self.assertEqual(
alignment[1],
"CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAACATTAAAAGAT",
)
self.assertEqual(
alignment[2],
"CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGGGAAATCGTCAATATTAAAAGGT",
)
self.assertEqual(
alignment[3],
"TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGGGAAATGGTCAATCTTAAAAGGT",
)
self.assertEqual(
alignment[4],
"CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAATATTAAAAGGT",
)
self.check_reading_writing(path)
self.assertTrue(
numpy.array_equal(
alignment.coordinates,
numpy.array([[0, 60], [0, 60], [0, 60], [0, 60], [0, 60]]),
)
)