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
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
|
import xml.dom.minidom
from unittest import TestCase
from cogent3.parse.blast_xml import (
HIT_XML_FIELDNAMES,
HSP_XML_FIELDNAMES,
BlastXMLResult,
get_tag,
minimal_blast_parser_7,
parse_header,
parse_hit,
parse_hsp,
parse_parameters,
)
class GetTagTests(TestCase):
"""Tests for the auxiliary function evaluating the tag objects."""
def setUp(self):
self.single_tag = xml.dom.minidom.parseString(
"<outer>bla <inner>content</inner>bla</outer>"
)
self.double_tag = xml.dom.minidom.parseString(
"<outer><inner>first content</inner><inner>second content</inner></outer>"
)
self.empty_tag = xml.dom.minidom.parseString("<outer></outer>")
def test_get_tag_works(self):
self.assertEqual(get_tag(self.single_tag, "inner"), "content")
self.assertEqual(get_tag(self.double_tag, "inner"), "first content")
self.assertEqual(get_tag(self.empty_tag, "inner"), None)
self.assertEqual(
get_tag(self.empty_tag, "inner", "blue elephant"), "blue elephant"
)
self.assertEqual(get_tag(self.single_tag, "non-existing tag"), None)
self.assertEqual(
get_tag(self.single_tag, "non-existing tag", "pink elephant"),
"pink elephant",
)
self.assertEqual(get_tag(self.single_tag, "inner"), "content")
def test_get_tag_fail(self):
"""Make sure the tag and name parameters are in the proper types."""
self.assertRaises(AttributeError, get_tag, None, "h1")
self.assertRaises(
AttributeError, get_tag, "<h1>This is not a XML tag object</h1>", "h1"
)
class MinimalBlastParser7Tests(TestCase):
"""Tests for the functions required by the Blast XML parsers."""
def setUp(self):
self.hit1 = xml.dom.minidom.parseString(HIT_WITH_ONE_HSP)
self.hit2 = xml.dom.minidom.parseString(HIT_WITH_TWO_HSPS)
self.hsp1 = xml.dom.minidom.parseString(HSP_ONE)
self.hsp2 = xml.dom.minidom.parseString(HSP_TWO)
self.hsp_gaps = xml.dom.minidom.parseString(HSP_WITH_GAPS)
self.param = xml.dom.minidom.parseString(PARAM_XML)
self.header = xml.dom.minidom.parseString(HEADER_XML)
self.complete = xml.dom.minidom.parseString(HEADER_COMPLETE)
def test_parse_header(self):
"""Fields from XML header tag should be available as dict."""
data = parse_header(self.header)
self.assertEqual(data.get("application"), "my Grandma")
self.assertEqual(data.get("version"), "has")
self.assertEqual(data.get("reference"), "furry")
self.assertEqual(data.get("query_letters"), 27)
self.assertEqual(data.get("database"), "Cats")
def test_parse_parameters(self):
"""Fields from XML parameter tag should be available as dict."""
data = parse_parameters(self.param)
self.assertEqual(data.get("matrix"), "BLOSUM62")
self.assertEqual(data.get("expect"), "10")
self.assertEqual(data.get("gap_open_penalty"), 11.1)
self.assertEqual(data.get("gap_extend_penalty"), 22.2)
self.assertEqual(data.get("filter"), "F")
def test_parse_header_complete(self):
"""Fields from header+param tag should be available as dict."""
# try to process header with parameters etc in the XML
data = parse_header(self.complete)
self.assertEqual(data.get("database"), "Cats")
self.assertEqual(data.get("matrix"), "BLOSUM62")
def test_parse_hit(self):
"""Should return a list with all values for a hit+hsp."""
data = parse_hit(self.hit1)
self.assertEqual(len(data), 1)
d = dict(list(zip(HIT_XML_FIELDNAMES, data[0])))
self.assertEqual(d["SUBJECT_ID"], "gi|148670104|gb|EDL02051.1|")
self.assertEqual(
d["HIT_DEF"],
"insulin-like growth factor 2 receptor, isoform CRA_c [Mus musculus]",
)
self.assertEqual(d["HIT_ACCESSION"], "2001")
self.assertEqual(int(d["HIT_LENGTH"]), 707)
# check hit with more HSPs
data = parse_hit(self.hit2)
self.assertEqual(len(data), 2)
self.assertNotEqual(data[0], data[1])
def test_parse_hsp(self):
"""Should return list with all values for a hsp."""
data = parse_hsp(self.hsp1)
d = dict(list(zip(HSP_XML_FIELDNAMES, data)))
self.assertEqual(float(d["BIT_SCORE"]), 1023.46)
self.assertEqual(float(d["SCORE"]), 2645)
self.assertEqual(float(d["E_VALUE"]), 0.333)
self.assertEqual(int(d["QUERY_START"]), 4)
self.assertEqual(int(d["QUERY_END"]), 18)
self.assertEqual(int(d["SUBJECT_START"]), 5)
self.assertEqual(int(d["SUBJECT_END"]), 19)
self.assertEqual(int(d["GAP_OPENINGS"]), 0)
self.assertEqual(int(d["ALIGNMENT_LENGTH"]), 14)
self.assertEqual(d["QUERY_ALIGN"], "ELEPHANTTHISISAHITTIGER")
self.assertEqual(d["MIDLINE_ALIGN"], "ORCA-WHALE")
self.assertEqual(d["SUBJECT_ALIGN"], "SEALSTHIS---HIT--GER")
class BlastXmlResultTests(TestCase):
"""Tests parsing of output of Blast with output mode 7 (XML)."""
def setUp(self):
self.result = BlastXMLResult(COMPLETE_XML, xml=True)
def test_options(self):
"""Constructor should take parser as an option."""
result = BlastXMLResult(COMPLETE_XML, parser=minimal_blast_parser_7)
self.assertEqual(len(list(result.keys())), 1)
# make sure whether normal Blast parser still works upon code merge!
def test_parsed_query_sequence(self):
"""The result dict should have one query sequence as a key."""
# The full query sequence is not given in the XML file.
# Thus it is not checked explicitly, only whether there is
# exactly one found.
self.assertEqual(len(list(self.result.keys())), 1)
def test_parsed_iterations(self):
"""The result should have the right number of iterations."""
n_iter = 0
for query_id, hits in self.result.iter_hits_by_query():
n_iter += 1
self.assertEqual(n_iter, 1)
def test_parsed_hsps(self):
"""The result should have the right number of hsps."""
n_hsps = 0
for query_id, hsps in self.result.iter_hits_by_query():
n_hsps += len(hsps)
self.assertEqual(n_hsps, 3)
def test_parse_hit_details(self):
"""The result should have data from hit fields."""
for query in self.result:
first_hsp = self.result[query][0][0]
self.assertEqual(first_hsp["SUBJECT_ID"], "gi|148670104|gb|EDL02051.1|")
self.assertEqual(
first_hsp["HIT_DEF"],
"insulin-like growth factor 2 receptor, isoform CRA_c [Mus musculus]",
)
self.assertEqual(first_hsp["HIT_ACCESSION"], "2001")
self.assertEqual(first_hsp["HIT_LENGTH"], 707)
def test_parse_hsp_details(self):
"""The result should have data from hsp fields."""
for query in self.result:
# should check integers in next version.
first_hsp = self.result[query][0][0]
self.assertEqual(first_hsp["QUERY ID"], 1)
self.assertEqual(first_hsp["BIT_SCORE"], "1023.46")
self.assertEqual(first_hsp["SCORE"], "2645")
self.assertEqual(first_hsp["E_VALUE"], "0.333")
self.assertEqual(first_hsp["QUERY_START"], "4")
self.assertEqual(first_hsp["QUERY_END"], "18")
self.assertEqual(first_hsp["QUERY_ALIGN"], "ELEPHANTTHISISAHITTIGER")
self.assertEqual(first_hsp["MIDLINE_ALIGN"], "ORCA-WHALE")
self.assertEqual(first_hsp["SUBJECT_ALIGN"], "SEALSTHIS---HIT--GER")
self.assertEqual(first_hsp["SUBJECT_START"], "5")
self.assertEqual(first_hsp["SUBJECT_END"], "19")
self.assertEqual(first_hsp["PERCENT_IDENTITY"], "55")
self.assertEqual(first_hsp["POSITIVE"], "555")
self.assertEqual(first_hsp["GAP_OPENINGS"], 0)
self.assertEqual(first_hsp["ALIGNMENT_LENGTH"], "14")
gap_hsp = self.result[query][0][1]
self.assertEqual(gap_hsp["GAP_OPENINGS"], "33")
def test_best_hits_by_query(self):
"""Exercising best hits"""
q, best_hits = next(self.result.best_hits_by_query())
best_hit = best_hits[0]
self.assertEqual(best_hit["QUERY ID"], 1)
self.assertEqual(best_hit["BIT_SCORE"], "1023.46")
self.assertEqual(best_hit["SCORE"], "2645")
self.assertEqual(best_hit["E_VALUE"], "0.333")
self.assertEqual(best_hit["QUERY_START"], "4")
self.assertEqual(best_hit["QUERY_END"], "18")
self.assertEqual(best_hit["QUERY_ALIGN"], "ELEPHANTTHISISAHITTIGER")
self.assertEqual(best_hit["MIDLINE_ALIGN"], "ORCA-WHALE")
self.assertEqual(best_hit["SUBJECT_ALIGN"], "SEALSTHIS---HIT--GER")
self.assertEqual(best_hit["SUBJECT_START"], "5")
self.assertEqual(best_hit["SUBJECT_END"], "19")
self.assertEqual(best_hit["PERCENT_IDENTITY"], "55")
self.assertEqual(best_hit["POSITIVE"], "555")
self.assertEqual(best_hit["GAP_OPENINGS"], 0)
self.assertEqual(best_hit["ALIGNMENT_LENGTH"], "14")
def test_best_hits_unique(self):
"""The result should never contain identical hits"""
records = [h for _, h in self.result.best_hits_by_query(n=5)][0]
self.assertEqual(len(records), 3)
values = {tuple(h.values()) for h in records}
self.assertEqual(len(values), 3)
HSP_XML = """
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>1023.46</Hsp_bit-score>
<Hsp_score>2645</Hsp_score>
<Hsp_evalue>0.333</Hsp_evalue>
<Hsp_query-from>4</Hsp_query-from>
<Hsp_query-to>18</Hsp_query-to>
<Hsp_hit-from>5</Hsp_hit-from>
<Hsp_hit-to>19</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>55</Hsp_identity>
%s
<Hsp_positive>555</Hsp_positive>
<Hsp_align-len>14</Hsp_align-len>
<Hsp_qseq>ELEPHANTTHISISAHITTIGER</Hsp_qseq>
<Hsp_hseq>SEALSTHIS---HIT--GER</Hsp_hseq>
<Hsp_midline>ORCA-WHALE</Hsp_midline>
</Hsp>
"""
HSP_ONE = HSP_XML % ""
HSP_WITH_GAPS = HSP_XML % "<Hsp_gaps>33</Hsp_gaps>"
HSP_TWO = """
<Hsp>
<Hsp_num>2</Hsp_num>
<Hsp_bit-score>1023.46</Hsp_bit-score>
<Hsp_score>2645</Hsp_score>
<Hsp_evalue>0.333</Hsp_evalue>
<Hsp_query-from>6</Hsp_query-from>
<Hsp_query-to>22</Hsp_query-to>
<Hsp_hit-from>5</Hsp_hit-from>
<Hsp_hit-to>23</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>55</Hsp_identity>
%s
<Hsp_positive>555</Hsp_positive>
<Hsp_align-len>18</Hsp_align-len>
<Hsp_qseq>EPHANT---THISISAHIT-TIGER</Hsp_qseq>
<Hsp_hseq>ALSWWWTHIS---HITW--GER</Hsp_hseq>
<Hsp_midline>ORCA-WHALE</Hsp_midline>
</Hsp>
"""
HIT_XML = """
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|148670104|gb|EDL02051.1|</Hit_id>
<Hit_def>insulin-like growth factor 2 receptor, isoform CRA_c [Mus musculus]</Hit_def>
<Hit_accession>2001</Hit_accession>
<Hit_len>707</Hit_len>
<Hit_hsps>
%s
</Hit_hsps>
</Hit>
"""
HIT_WITH_ONE_HSP = HIT_XML % HSP_ONE
HIT_WITH_TWO_HSPS = HIT_XML % (HSP_WITH_GAPS + HSP_TWO)
PARAM_XML = """
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>10</Parameters_expect>
<Parameters_gap-open>11.1</Parameters_gap-open>
<Parameters_gap-extend>22.2</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
"""
HEADER_XML = """
<BlastOutput>
<BlastOutput_program>my Grandma</BlastOutput_program>
<BlastOutput_version>has</BlastOutput_version>
<BlastOutput_db>Cats</BlastOutput_db>
<BlastOutput_reference>furry</BlastOutput_reference>
<BlastOutput_query-len>27</BlastOutput_query-len>
%s
</BlastOutput>
"""
HIT_PREFIX = """
<BlastOutput_iterations>
<Iteration>
<Iteration_hits>
"""
HIT_SUFFIX = """
</Iteration_hits>
</Iteration>
</BlastOutput_iterations>
"""
HEADER_COMPLETE = HEADER_XML % (
PARAM_XML + HIT_PREFIX + HIT_WITH_ONE_HSP + HIT_WITH_TWO_HSPS + HIT_SUFFIX
)
COMPLETE_XML = (
"""<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
"""
+ HEADER_COMPLETE
)
|
