1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
|
# Copyright 2010 by Thomas Schmitt. 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.
import unittest
import sys
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio._py3k import StringIO
test_files = {
"dna": ["SeqXML/dna_example.xml", 4],
"rna": ["SeqXML/rna_example.xml", 5],
"protein": ["SeqXML/protein_example.xml", 5],
"globalSpecies": ["SeqXML/global_species_example.xml", 2],
}
corrupt_files = [
"SeqXML/corrupt_example1.xml",
"SeqXML/corrupt_example2.xml",
]
def assert_equal_records(testCase, record_a, record_b):
testCase.assertEqual(record_a.id, record_b.id)
testCase.assertEqual(record_a.name, record_b.name)
testCase.assertEqual(record_a.description, record_b.description)
testCase.assertEqual(str(record_a.seq), str(record_b.seq))
testCase.assertEqual(record_a.dbxrefs, record_b.dbxrefs)
testCase.assertEqual(record_a.annotations, record_a.annotations)
class TestSimpleRead(unittest.TestCase):
def test_check_SeqIO(self):
"""Files readable using parser via SeqIO."""
for key in test_files:
records = list(SeqIO.parse(test_files[key][0], "seqxml"))
self.assertEqual(len(records), test_files[key][1])
class TestDetailedRead(unittest.TestCase):
records = {}
def setUp(self):
for key in test_files:
self.records[key] = list(SeqIO.parse(test_files[key][0], "seqxml"))
def test_special_characters_desc(self):
"""Read special XML characters in description."""
self.assertEqual(self.records["dna"][2].description, u'some special characters in the description\n<tag> "quoted string"')
# TODO - Fix this failure under Windows with Python 3.1 and 3.2
if not (sys.platform == "win32" and sys.version_info[0] >= 3):
def test_unicode_characters_desc(self):
"""Test special unicode characters in the description."""
self.assertEqual(self.records["rna"][2].description, u"\u00E5\u00C5\u00FC\u00F6\u00D6\u00DF\u00F8\u00E4\u00A2\u00A3$\u20AC\u9999\u80A0")
def test_full_characters_set_read(self):
"""Read full characters set for each type"""
self.assertEqual(str(self.records["dna"][1].seq), "ACGTMRWSYKVHDBXN.-")
self.assertEqual(str(self.records["rna"][1].seq), "ACGUMRWSYKVHDBXN.-")
self.assertEqual(str(self.records["protein"][1].seq), "ABCDEFGHIJKLMNOPQRSTUVWXYZ.-*")
def test_duplicated_property(self):
"""Read property with multiple values"""
self.assertEqual(self.records["protein"][2].annotations["test"], [u"1", u"2", u"3"])
def test_duplicated_dbxref(self):
"""Read multiple cross references to a single source"""
self.assertEqual(self.records["protein"][2].dbxrefs, [u"someDB:G001", u"someDB:G002"])
def test_read_minimal_required(self):
"""Check minimal record."""
minimalRecord = SeqRecord(id="test", seq=Seq("abc"))
minimalRecord.annotations["source"] = u"Ensembl"
self.assertEqual(self.records["rna"][3].name, minimalRecord.name)
self.assertEqual(self.records["dna"][3].annotations, minimalRecord.annotations)
self.assertEqual(self.records["rna"][3].dbxrefs, minimalRecord.dbxrefs)
self.assertEqual(self.records["protein"][3].description, minimalRecord.description)
def test_local_species(self):
"""Check local species."""
self.assertEqual(self.records["rna"][1].annotations["organism"], "Mus musculus")
self.assertEqual(self.records["rna"][1].annotations["ncbi_taxid"], "10090")
self.assertEqual(self.records["rna"][0].annotations["organism"], "Gallus gallus")
self.assertEqual(self.records["rna"][0].annotations["ncbi_taxid"], "9031")
def test_global_species(self):
"""Check global species."""
self.assertEqual(self.records["globalSpecies"][0].annotations["organism"], "Mus musculus")
self.assertEqual(self.records["globalSpecies"][0].annotations["ncbi_taxid"], "10090")
self.assertEqual(self.records["globalSpecies"][1].annotations["organism"], "Homo sapiens")
self.assertEqual(self.records["globalSpecies"][1].annotations["ncbi_taxid"], "9606")
def test_local_source_definition(self):
"""Check local source."""
self.assertEqual(self.records["protein"][4].annotations["source"], u"Uniprot")
def test_empty_description(self):
"""Check empty description."""
self.assertEqual(self.records["rna"][4].description, SeqRecord(id="", seq=Seq("")).description)
class TestReadAndWrite(unittest.TestCase):
def test_read_write_rna(self):
"""Read and write RNA."""
read1_records = list(SeqIO.parse(test_files["rna"][0], "seqxml"))
self._write_parse_and_compare(read1_records)
def test_read_write_dna(self):
"""Read and write DNA."""
read1_records = list(SeqIO.parse(test_files["dna"][0], "seqxml"))
self._write_parse_and_compare(read1_records)
def test_read_write_protein(self):
"""Read and write protein."""
read1_records = list(SeqIO.parse(test_files["protein"][0], "seqxml"))
self._write_parse_and_compare(read1_records)
def test_read_write_globalSpecies(self):
"""Read and write global species."""
read1_records = list(SeqIO.parse(test_files["globalSpecies"][0], "seqxml"))
self._write_parse_and_compare(read1_records)
def _write_parse_and_compare(self, read1_records):
handle = StringIO()
SeqIO.write(read1_records, handle, "seqxml")
handle.seek(0)
read2_records = list(SeqIO.parse(handle, "seqxml"))
self.assertEqual(len(read1_records), len(read2_records))
for record1, record2 in zip(read1_records, read2_records):
assert_equal_records(self, record1, record2)
def test_write_species(self):
"""Test writing species from annotation tags."""
record = SeqIO.read("SwissProt/sp016", "swiss")
self.assertEqual(record.annotations["organism"], "Homo sapiens (Human)")
self.assertEqual(record.annotations["ncbi_taxid"], ["9606"])
handle = StringIO()
SeqIO.write(record, handle, "seqxml")
handle.seek(0)
output = handle.getvalue()
self.assertTrue("Homo sapiens (Human)" in output)
self.assertTrue("9606" in output)
if '<species name="Homo sapiens (Human)" ncbiTaxID="9606"/>' in output:
# Good, but don't get this (do we?)
pass
elif '<species name="Homo sapiens (Human)" ncbiTaxID="9606"></species>' in output:
# Not as concise, but fine (seen on C Python)
pass
elif '<species ncbiTaxID="9606" name="Homo sapiens (Human)"></species>' in output:
# Jython uses a different order
pass
elif '<species ncbiTaxID="9606" name="Homo sapiens (Human)"/>' in output:
# This would be fine too, but don't get this (do we?)
pass
else:
raise ValueError("Mising expected <species> tag: %r" % output)
class TestReadCorruptFiles(unittest.TestCase):
def test_for_errors(self):
"""Handling of corrupt files."""
for filename in corrupt_files:
iterator = SeqIO.parse(filename, "seqxml")
self.assertRaises(ValueError, next, iterator)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
