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
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
|
# Copyright 2008-2016 by Peter Cock. 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.
"""Testing online code for fetching NCBI qblast.
Uses Bio.Blast.NCBIWWW.qblast() to run some online blast queries, get XML
blast results back, and then checks Bio.Blast.NCBIXML.parse() can read them.
Goals:
- Make sure that all retrieval is working as expected.
- Make sure we can parse the latest XML format being used by the NCBI.
"""
from __future__ import print_function
import unittest
from Bio._py3k import HTTPError
from Bio._py3k import StringIO
from Bio import MissingExternalDependencyError
# We want to test these:
from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML
import requires_internet
requires_internet.check()
#####################################################################
# List of qblast requests stored as a tuple of parameters:
# - program
# - database
# - query identifier or sequence
# - expectation value threshold
# - Entrez filter string (or None)
# - list of hit identifiers expected to be found (or None if expect 0)
print("Checking Bio.Blast.NCBIWWW.qblast() with various queries")
class TestQblast(unittest.TestCase):
def test_blastp_nr_actin(self):
# Simple protein blast filtered for rat only, using protein
# GI:160837788 aka NP_075631.2
# the actin related protein 2/3 complex, subunit 1B [Mus musculus]
self.run_qblast("blastp", "nr", "NP_075631.2", 0.001,
"rat [ORGN]", {'megablast': 'FALSE'},
['9506405', '13592137', '37589612', '149064087', '56912225'])
def test_pcr_primers(self):
# This next example finds PCR primer matches in Chimpanzees, e.g. BRCA1:
self.run_qblast("blastn", "nr", "GTACCTTGATTTCGTATTC" + ("N" * 30) + "GACTCTACTACCTTTACCC",
10, "pan [ORGN]", {'megablast': 'FALSE'},
["XM_009432096.3", "XM_009432102.3", "XM_009432101.3",
"XM_016930487.2", "XM_009432104.3", "XM_009432099.3",
"XR_001710553.2", "XM_016930485.2", "XM_009432089.3",
"XM_016930484.2"])
def test_orchid_est(self):
# Try an orchid EST (nucleotide) sequence against NR using BLASTX
self.run_qblast("blastx", "nr",
""">gi|116660609|gb|EG558220.1|EG558220 CR02019H04 Leaf CR02 cDNA library Catharanthus roseus cDNA clone CR02019H04 5', mRNA sequence
CTCCATTCCCTCTCTATTTTCAGTCTAATCAAATTAGAGCTTAAAAGAATGAGATTTTTAACAAATAAAA
AAACATAGGGGAGATTTCATAAAAGTTATATTAGTGATTTGAAGAATATTTTAGTCTATTTTTTTTTTTT
TCTTTTTTTGATGAAGAAAGGGTATATAAAATCAAGAATCTGGGGTGTTTGTGTTGACTTGGGTCGGGTG
TGTATAATTCTTGATTTTTTCAGGTAGTTGAAAAGGTAGGGAGAAAAGTGGAGAAGCCTAAGCTGATATT
GAAATTCATATGGATGGAAAAGAACATTGGTTTAGGATTGGATCAAAAAATAGGTGGACATGGAACTGTA
CCACTACGTCCTTACTATTTTTGGCCGAGGAAAGATGCTTGGGAAGAACTTAAAACAGTTTTAGAAAGCA
AGCCATGGATTTCTCAGAAGAAAATGATTATACTTCTTAATCAGGCAACTGATATTATCAATTTATGGCA
GCAGAGTGGTGGCTCCTTGTCCCAGCAGCAGTAATTACTTTTTTTTCTCTTTTTGTTTCCAAATTAAGAA
ACATTAGTATCATATGGCTATTTGCTCAATTGCAGATTTCTTTCTTTTGTGAATG""",
0.0000001, None, {'megablast': 'FALSE'},
["21554275", "18409071", "296087288", "566183510"])
def test_discomegablast(self):
self.run_qblast("blastn", "nr",
""">some sequence
ATGAAGATCTTCCAGATCCAGTGCAGCAGCTTCAAGGAGAGCAGGTGGCAGAAGAGCAAGTGCGACAACT
GCCTGAAGTTCCACATCGACATCAACAACAACAGCAAGACCAGCAACACCGACACCGACTTCGACGCCAA
CACCAACATCAACAGCAACATCAACAGCAACATCAACAGCAACATCAACATCAACAACAGCGGCAACAAC
AACAAGAACAGCAACAACATCGAGATCACCGAGAACATCGACAACAAGGCCAAGATCATCAACAAGCACA
TCAAGACCATCACCAACAGCAAGCCCATCCCCATCCCCATCCCCACCCCCACCCCCATCAGCATCAAGGA
GAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGATG
AAGAGCACCATCAACCTGAGGAGCGAGGACACCACCAGCAACAAGAGCACCATCGTGTTCACCGAGTGCC
TGGAGTACAAGGGCCACCAGTGGAGGCCCAACATCTGCGTGACCTGCTTCAGCCCCAAGAACAAGCACAA
GAACGTGCTGCCCGAGACCAGCACCCCCCTGATCAGCCAGAGCAGCCAGACCAGCACCATCACCCCCAGC
AGCAGCAGCACCAGCACCAGCACCAGCAGCATCAGCACCCACAAGACCGCCAACAACAAGACCGTGATCA
CCTACATCAGCAGCACCACCACCACCACCACCACCAGCAGCAGCAGCAGCAGCCCCCCCAGCAGCAGCAT
CGCCGGCATCACCAACCCCACCAGCAGGAGCAGCAGCCCCATCCTGAAGAGCGTGCCCCCCAGCGCCTAC
AGCAACGTGGTGATCCCCATCAACAACATCAACAACAGCAACAGCAACAGCAGCAGCGGCGGCGGCAACA
ACAACAACAAGAGCATCAGCACCCCCAGCAGCCCCATCATCAGCAGGCCCATCACCAACAAGATCAACAA
CAACAACAACAACAACCAGCCCCAGCTGCACTACAACCAGCCCCAGAGCAGCAGCGTGAGCACCACCAGC
AGCCCCATCATCAGGCCCGTGCTGAGGAGGCAGTTCCAGAGCTTCCCCAGCAACCCCAAGATCAGCAAGG
CCATCCTGGAGCAGTGCAACATCATCAACAACAACAGCAACAGCAACAACAGCAACAACAAGGACCCCGT
GATCCTGTGCAAGTACACCATCGAGAGCCAGCCCAAGAGCAACATCAGCGTGCTGAAGCCCACCCTGGTG
GAGTTCATCAACCAGCCCGACAGCAAGGACGACGAGAGCAGCGTGAAGAGCCCCCCCCTGCCCGTGGAGA
GCCAGCCCATCTTCAACAGCAAGCAGAGCGCCACCATGGACGGCATCACCACCCACAAGAGCGTGAGCAT
CACCATCAGCACCAGCACCAGCCCCAGCAGCACCACCACCACCACCAGCACCACCACCAGCATCATCGCC
GAGGAGCCCAGCAGCCCCATCCTGCCCACCGCCAGCCCCAGCAGCAGCAGCAGCAGCATCATCACCACCG
CCACCGCCAGCACCATCCCCATGAGCCCCAGCCTGCCCAGCATCCCCTTCCACGAGTTCGAGACCATGGA
GAGCAGCACCACCACCACCCTGCTGAGCGAGAACAACGGCGGCGGCGGCGGCAGCAGCTGCAACGACAAC
AGCAGGAGGAACAGCCTGAACATCCTGCCCCTGAGGCTGAAGAGCTTCAGCTTCAGCGCCCCCCAGAGCG
ACAGCATGATCGAGCAGCCCGAGGACGACCCCTTCTTCGACTTCGAGGACCTGAGCGACGACGACGACAG
CAACGACAACGACGACGAGGAGCTGAAGGAGATCAACGGCGAGAAGATCATCCAGCAGAACGACCTGACC
CCCACCACCACCATCACCAGCACCACCACCATCCTGCAGAGCCCCACCCTGGAGAAGACCCTGAGCACCA
CCACCACCACCACCATCCCCAGCCCCAGCACCAACAGCAGGAGCATCTGCAACACCCTGATGGACAGCAC
CGACAGCATCAACAACACCAACACCAACACCAACACCAACACCAACACCAACACCAACACCAACACCAAC
ACCAACACCAACACCAACACCAACGCCAACATCAACAACAAGGTGAGCACCACCACCACCACCACCACCA
CCAAGAGGAGGAGCCTGAAGATGGACCAGTTCAAGGAGAAGGAGGACGAGTGGGACCAGGGCGTGGACCT
GACCAGCTTCCTGAAGAGGAAGCCCACCCTGCAGAGGGACTTCAGCTACTGCAACAACAAGGTGATGGAG
ATCAGCAGCGTGAAGGAGGAGGCCAAGAGGCTGCACGGCGGCACCGGCTACATCCACCAGTTCGCCTTCG
AGGCCTTCAAGGACATCCTGGAGGCCAAGCAGACCCAGATCAACAGGGCCTTCTGCAGCCAGAAGATCGA
CGCCCCCGACTGCGAGATGCTGATCAACGAGATCAACACCGCCAAGAAGCTGCTGGAGGACCTGCTGGAG
CTGAACAGCAACAGCAGCGGCAGCGGCAACAACAGCAACGACAACAGCGGCAGCAGCAGCCCCAGCAGCA
GCAAGACCAACACCCTGAACCAGCAGAGCATCTGCATCAAGAGCGAGATCCAACGATACGTTGAAATTCG
CTTGTGTGCCACTGGTAAATCCACCCCCCCTAAGCCTCTAATAGGGAGACCTTAG""",
0.0000001, None, {
'template_type': 0,
'template_length': 18,
'megablast': 'on',
}, ['XM_635681.1', 'XM_008496783.1'])
def run_qblast(self, program, database, query, e_value, entrez_filter, additional_args, expected_hits):
try:
if program == "blastn":
# Check the megablast parameter is accepted
handle = NCBIWWW.qblast(program, database, query,
alignments=10, descriptions=10,
hitlist_size=10,
entrez_query=entrez_filter,
expect=e_value,
**additional_args)
else:
handle = NCBIWWW.qblast(program, database, query,
alignments=10, descriptions=10,
hitlist_size=10,
entrez_query=entrez_filter,
expect=e_value,
**additional_args)
except HTTPError:
# e.g. a proxy error
raise MissingExternalDependencyError("internet connection failed")
record = NCBIXML.read(handle)
if record.query == "No definition line":
# We used a sequence as the query
self.assertEqual(len(query), record.query_letters)
elif query.startswith(">"):
# We used a FASTA record as the query
expected = query[1:].split("\n", 1)[0]
self.assertEqual(expected, record.query)
elif record.query_id.startswith("Query_") and len(query) == record.query_letters:
# We used a sequence as the entry and it was given a placeholder name
pass
else:
# We used an identifier as the query
self.assertIn(query, record.query_id.split("|"),
"Expected %r within query_id %r" % (query, record.query_id))
# Check the recorded input parameters agree with those requested
self.assertEqual(float(record.expect), e_value)
self.assertEqual(record.application.lower(), program)
self.assertTrue(len(record.alignments) <= 10)
self.assertTrue(len(record.descriptions) <= 10)
# Check the expected result(s) are found in the alignments
if expected_hits is None:
self.assertEqual(len(record.alignments), 0) # Expected no alignments!
else:
self.assertTrue(len(record.alignments) > 0) # Expected some alignments!
found_result = False
for expected_hit in expected_hits:
for alignment in record.alignments:
if expected_hit in alignment.hit_id.split("|"):
found_result = True
break
if len(expected_hits) == 1:
print("Update this test to have some redundancy...")
for alignment in record.alignments:
print(alignment.hit_id)
self.assertTrue(found_result,
"Missing all expected hits (%s), instead have: %s"
% (", ".join(expected_hits),
", ".join(a.hit_id for a in record.alignments)))
# Check the expected result(s) are found in the descriptions
if expected_hits is None:
self.assertEqual(len(record.descriptions), 0) # Expected no descriptions!
else:
self.assertTrue(len(record.descriptions) > 0) # Expected some descriptions!
found_result = False
for expected_hit in expected_hits:
for descr in record.descriptions:
if expected_hit == descr.accession \
or expected_hit in descr.title.split(None, 1)[0].split("|"):
found_result = True
break
assert found_result, "Missing all of %s in descriptions" % expected_hit
self.assertTrue(found_result)
def test_parse_qblast_ref_page(self):
with open("Blast/html_msgid_29_blastx_001.html", "r") as f:
handle = StringIO(f.read())
self.assertRaises(ValueError, NCBIWWW._parse_qblast_ref_page, handle)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
