forked from biopython/biopython
/
test_SearchIO_hhsuite2_text.py
549 lines (485 loc) · 21.4 KB
/
test_SearchIO_hhsuite2_text.py
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
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
# Copyright 2019 by Jens Thomas. 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.
"""Tests for SearchIO HhsuiteIO parsers."""
import os
import unittest
from Bio.SearchIO import parse
# test case files are in the Blast directory
TEST_DIR = "HHsuite"
FMT = "hhsuite2-text"
def get_file(filename):
"""Return the path of a test file."""
return os.path.join(TEST_DIR, filename)
class HhsuiteCases(unittest.TestCase):
"""Test hhsuite2 output."""
def test_2uvo(self):
"""Parsing 2uvo."""
txt_file = get_file("2uvo_hhblits.hhr")
qresults = parse(txt_file, FMT)
# test first and only qresult
qresult = next(qresults)
num_hits = 16
self.assertEqual("HHSUITE", qresult.program)
self.assertEqual("2UVO:A|PDBID|CHAIN|SEQUENCE", qresult.id)
self.assertEqual(171, qresult.seq_len)
self.assertEqual(num_hits, len(qresult))
hit = qresult[0]
self.assertEqual("2uvo_A", hit.id)
self.assertEqual(
"Agglutinin isolectin 1; carbohydrate-binding protein, hevein domain, chitin-binding,"
" GERM agglutinin, chitin-binding protein; HET: NDG NAG GOL; 1.40A {Triticum aestivum}"
" PDB: 1wgc_A* 2cwg_A* 2x3t_A* 4aml_A* 7wga_A 9wga_A 2wgc_A 1wgt_A 1k7t_A* 1k7v_A* 1k7u_A"
" 2x52_A* 1t0w_A*",
hit.description,
)
self.assertTrue(hit.is_included)
self.assertEqual(3.7e-34, hit.evalue)
self.assertEqual(210.31, hit.score)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertTrue(hsp.is_included)
self.assertEqual(0, hsp.output_index)
self.assertEqual(99.95, hsp.prob)
self.assertEqual(210.31, hsp.score)
self.assertEqual(3.7e-34, hsp.evalue)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(171, hsp.hit_end)
self.assertEqual(0, hsp.query_start)
self.assertEqual(171, hsp.query_end)
self.assertEqual(
"ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYC"
"GAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCS"
"KWGSCGIGPGYCGAGCQSGGCDG",
str(hsp.hit.seq),
)
self.assertEqual(
"ERCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYC"
"GAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCS"
"KWGSCGIGPGYCGAGCQSGGCDG",
str(hsp.query.seq),
)
# Check last hit
hit = qresult[num_hits - 1]
self.assertEqual("4z8i_A", hit.id)
self.assertEqual(
"BBTPGRP3, peptidoglycan recognition protein 3; chitin-binding domain, "
"AM hydrolase; 2.70A {Branchiostoma belcheri tsingtauense}",
hit.description,
)
self.assertTrue(hit.is_included)
self.assertEqual(0.11, hit.evalue)
self.assertEqual(36.29, hit.score)
self.assertEqual(2, len(hit))
# Check we can get the original last HSP from the file.
num_hsps = 32
self.assertEqual(num_hsps, len(qresult.hsps))
hsp = qresult.hsps[-1]
self.assertTrue(hsp.is_included)
self.assertEqual(num_hsps - 1, hsp.output_index)
self.assertEqual(2.6, hsp.evalue)
self.assertEqual(25.90, hsp.score)
self.assertEqual(40.43, hsp.prob)
self.assertEqual(10, hsp.hit_start)
self.assertEqual(116, hsp.hit_end)
self.assertEqual(53, hsp.query_start)
self.assertEqual(163, hsp.query_end)
self.assertEqual(
"XCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCXXX--XXXCXXXXCCXXXXXCXXXXXXCXXXCXXXXCXXXXXCX"
"XX--XXXCXXXXCCXXXXXCXXXXXXCXXX",
str(hsp.hit.seq),
)
self.assertEqual(
"TCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCG"
"KDAGGRVCTNNYCCSKWGSCGIGPGYCGAG",
str(hsp.query.seq),
)
def test_2uvo_onlyheader(self):
"""Parsing 4uvo with only header present."""
txt_file = get_file("2uvo_hhblits_onlyheader.hhr")
qresults = parse(txt_file, FMT)
with self.assertRaises(RuntimeError):
next(qresults)
def test_2uvo_emptytable(self):
"""Parsing 4uvo with empty results table."""
txt_file = get_file("2uvo_hhblits_emptytable.hhr")
qresults = parse(txt_file, FMT)
with self.assertRaises(RuntimeError):
next(qresults)
def test_allx(self):
"""Parsing allx.hhr file."""
txt_file = get_file("allx.hhr")
qresults = parse(txt_file, FMT)
# test first and only qresult
qresult = next(qresults)
num_hits = 10
self.assertEqual("HHSUITE", qresult.program)
self.assertEqual("Only X amino acids", qresult.id)
self.assertEqual(39, qresult.seq_len)
self.assertEqual(num_hits, len(qresult))
hit = qresult[0]
self.assertEqual("1klr_A", hit.id)
self.assertEqual(
"Zinc finger Y-chromosomal protein; transcription; NMR {Synthetic} SCOP: g.37.1.1 PDB: "
"5znf_A 1kls_A 1xrz_A* 7znf_A",
hit.description,
)
self.assertTrue(hit.is_included)
self.assertEqual(3.4e04, hit.evalue)
self.assertEqual(-0.01, hit.score)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertTrue(hsp.is_included)
self.assertEqual(0, hsp.output_index)
self.assertEqual(3.4e04, hsp.evalue)
self.assertEqual(-0.01, hsp.score)
self.assertEqual(0.04, hsp.prob)
self.assertEqual(23, hsp.hit_start)
self.assertEqual(24, hsp.hit_end)
self.assertEqual(38, hsp.query_start)
self.assertEqual(39, hsp.query_end)
self.assertEqual("T", str(hsp.hit.seq))
self.assertEqual("X", str(hsp.query.seq))
# Check last hit
hit = qresult[num_hits - 1]
self.assertEqual("1zfd_A", hit.id)
self.assertEqual(
"SWI5; DNA binding motif, zinc finger DNA binding domain; NMR {Saccharomyces cerevisiae}"
" SCOP: g.37.1.1",
hit.description,
)
self.assertTrue(hit.is_included)
self.assertEqual(3.6e04, hit.evalue)
self.assertEqual(0.03, hit.score)
self.assertEqual(1, len(hit))
# Check we can get the original last HSP from the file.
num_hsps = num_hits
self.assertEqual(num_hsps, len(qresult.hsps))
hsp = qresult.hsps[-1]
self.assertTrue(hsp.is_included)
self.assertEqual(num_hsps - 1, hsp.output_index)
self.assertEqual(3.6e04, hsp.evalue)
self.assertEqual(0.03, hsp.score)
self.assertEqual(0.03, hsp.prob)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(1, hsp.hit_end)
self.assertEqual(3, hsp.query_start)
self.assertEqual(4, hsp.query_end)
self.assertEqual("D", str(hsp.hit.seq))
self.assertEqual("X", str(hsp.query.seq))
def test_4y9h_nossm(self):
"""Parsing 4y9h_hhsearch_server_NOssm.hhr file."""
txt_file = get_file("4y9h_hhsearch_server_NOssm.hhr")
qresults = parse(txt_file, FMT)
# test first and only qresult
qresult = next(qresults)
num_hits = 29
self.assertEqual("HHSUITE", qresult.program)
self.assertEqual("4Y9H:A|PDBID|CHAIN|SEQUENCE", qresult.id)
self.assertEqual(226, qresult.seq_len)
self.assertEqual(num_hits, len(qresult))
hit = qresult[0]
self.assertEqual("5ZIM_A", hit.id)
self.assertEqual(
"Bacteriorhodopsin; proton pump, membrane protein, PROTON; HET: L2P, RET; 1.25A {Halobacterium"
" salinarum}; Related PDB entries: 1R84_A 1KG8_A 1KME_B 1KGB_A 1KG9_A 1KME_A 4X31_A 5ZIL_A 1E0P_A "
"4X32_A 5ZIN_A 1S53_B 1S51_B 1S53_A 1S54_A 1F50_A 1S54_B 1S51_A 1F4Z_A 5J7A_A 1S52_B 1S52_A 4Y9H_A "
"3T45_A 3T45_C 3T45_B 1C3W_A 1L0M_A",
hit.description,
)
self.assertTrue(hit.is_included)
self.assertEqual(2.1e-48, hit.evalue)
self.assertEqual(320.44, hit.score)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertTrue(hsp.is_included)
self.assertEqual(0, hsp.output_index)
self.assertEqual(2.1e-48, hsp.evalue)
self.assertEqual(320.44, hsp.score)
self.assertEqual(100.00, hsp.prob)
self.assertEqual(1, hsp.hit_start)
self.assertEqual(227, hsp.hit_end)
self.assertEqual(0, hsp.query_start)
self.assertEqual(226, hsp.query_end)
self.assertEqual(
"GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYAD"
"WLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRP"
"EVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG",
str(hsp.hit.seq),
)
self.assertEqual(
"GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYAD"
"WLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRP"
"EVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG",
str(hsp.query.seq),
)
# Check last hit
hit = qresult[num_hits - 1]
self.assertEqual("5ABB_Z", hit.id)
self.assertEqual(
"PROTEIN TRANSLOCASE SUBUNIT SECY, PROTEIN; TRANSLATION, RIBOSOME, MEMBRANE PROTEIN, "
"TRANSLOCON; 8.0A {ESCHERICHIA COLI}",
hit.description,
)
self.assertTrue(hit.is_included)
self.assertEqual(3.3e-05, hit.evalue)
self.assertEqual(51.24, hit.score)
self.assertEqual(1, len(hit))
# Check we can get the original last HSP from the file.
num_hsps = num_hits
self.assertEqual(num_hsps, len(qresult.hsps))
hsp = qresult.hsps[-1]
self.assertTrue(hsp.is_included)
self.assertEqual(num_hsps - 1, hsp.output_index)
self.assertEqual(3.3e-05, hsp.evalue)
self.assertEqual(51.24, hsp.score)
self.assertEqual(96.55, hsp.prob)
self.assertEqual(14, hsp.hit_start)
self.assertEqual(65, hsp.hit_end)
self.assertEqual(7, hsp.query_start)
self.assertEqual(59, hsp.query_end)
self.assertEqual(
"FWLVTAALLASTVFFFVERDRVS-AKWKTSLTVSGLVTGIAFWHYMYMRGVW", str(hsp.hit.seq)
)
self.assertEqual(
"LALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGY", str(hsp.query.seq)
)
def test_q9bsu1(self):
"""Parsing hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr file."""
txt_file = get_file("hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr")
qresults = parse(txt_file, FMT)
# test first and only qresult
qresult = next(qresults)
num_hits = 12
self.assertEqual("HHSUITE", qresult.program)
self.assertEqual(
"sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70"
" PE=1 SV=1",
qresult.id,
)
self.assertEqual(422, qresult.seq_len)
self.assertEqual(num_hits, len(qresult))
hit = qresult[0]
self.assertEqual("PF03676.13", hit.id)
self.assertEqual(
"UPF0183 ; Uncharacterised protein family (UPF0183)", hit.description
)
self.assertTrue(hit.is_included)
self.assertEqual(2e-106, hit.evalue)
self.assertEqual(822.75, hit.score)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertTrue(hsp.is_included)
self.assertEqual(0, hsp.output_index)
self.assertEqual(2e-106, hsp.evalue)
self.assertEqual(822.75, hsp.score)
self.assertEqual(100.00, hsp.prob)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(395, hsp.hit_end)
self.assertEqual(10, hsp.query_start)
self.assertEqual(407, hsp.query_end)
self.assertEqual(
"SLGNEQWEFTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLK"
"YCGVHFNSQAIAPTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGATVKR"
"MYIYSGNSLQDTKAPMMPLSCFLGNVYAESVDVLRDGTGPAGLRLRLLAAGCGPGLLADAKMRVFERSVYFGDSCQDVLS"
"MLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTNYPGHYNFNIYHRCEFKIP"
"LAIKKENADGQTE--TCTTYSKWDNIQELLGHPVEKPVVLHRSSSPNNTNPFGSTFCFGLQRMIFEVMQNNHIASVTLY",
str(hsp.query.seq),
)
self.assertEqual(
"EQWE----FALGMPLAQAISILQKHCRIIKNVQVLYSEQMPLSHDLILNLTQDGIKLLFDACNQRLKVIEVYDLTKVKLK"
"YCGVHFNSQAIAPTIEQIDQSFGATHPGVYNAAEQLFHLNFRGLSFSFQLDSWSEAPKYEPNFAHGLASLQIPHGATVKR"
"MYIYSGNNLQETKAPAMPLACFLGNVYAECVEVLRDGAGPLGLKLRLLTAGCGPGVLADTKVRAVERSIYFGDSCQDVLS"
"ALGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYYILGVDILFDSTTHLVKKFVLHTNFPGHYNFNIYHRCDFKIP"
"LIIKKDGADAHSEDCILTTYSKWDQIQELLGHPMEKPVVLHRSSSANNTNPFGSTFCFGLQRMIFEVMQNNHIASVTLY",
str(hsp.hit.seq),
)
# Check last hit
hit = qresult[num_hits - 1]
self.assertEqual("PF10049.8", hit.id)
self.assertEqual(
"DUF2283 ; Protein of unknown function (DUF2283)", hit.description
)
self.assertTrue(hit.is_included)
self.assertEqual(78, hit.evalue)
self.assertEqual(19.81, hit.score)
self.assertEqual(1, len(hit))
# Check we can get the original last HSP from the file.
num_hsps = 16
self.assertEqual(num_hsps, len(qresult.hsps))
hsp = qresult.hsps[-1]
self.assertTrue(hsp.is_included)
self.assertEqual(num_hsps - 1, hsp.output_index)
self.assertEqual(78, hsp.evalue)
self.assertEqual(19.81, hsp.score)
self.assertEqual(20.88, hsp.prob)
self.assertEqual(25, hsp.hit_start)
self.assertEqual(48, hsp.hit_end)
self.assertEqual(61, hsp.query_start)
self.assertEqual(85, hsp.query_end)
self.assertEqual("APNVIFDYDA-EGRIVGIELLDAR", str(hsp.hit.seq))
self.assertEqual("QDGIKLMFDAFNQRLKVIEVCDLT", str(hsp.query.seq))
def test_4p79(self):
"""Parsing 4p79_hhsearch_server_NOssm.hhr file."""
txt_file = get_file("4p79_hhsearch_server_NOssm.hhr")
qresults = parse(txt_file, FMT)
# test first and only qresult
qresult = next(qresults)
num_hits = 8
self.assertEqual("HHSUITE", qresult.program)
self.assertEqual("4P79:A|PDBID|CHAIN|SEQUENCE", qresult.id)
self.assertEqual(198, qresult.seq_len)
self.assertEqual(num_hits, len(qresult))
hit = qresult[0]
self.assertEqual("4P79_A", hit.id)
self.assertEqual(
"cell adhesion protein; cell adhesion, tight junction, membrane; HET: OLC"
", MSE; 2.4A {Mus musculus}",
hit.description,
)
self.assertTrue(hit.is_included)
self.assertEqual(6.8e-32, hit.evalue)
self.assertEqual(194.63, hit.score)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertTrue(hsp.is_included)
self.assertEqual(0, hsp.output_index)
self.assertEqual(6.8e-32, hsp.evalue)
self.assertEqual(194.63, hsp.score)
self.assertEqual(99.94, hsp.prob)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(198, hsp.hit_end)
self.assertEqual(0, hsp.query_start)
self.assertEqual(198, hsp.query_end)
self.assertEqual(
"GSEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQ"
"GCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKY"
"ELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR",
str(hsp.query.seq),
)
self.assertEqual(
"GSEFMSVAVETFGFFMSALGLLMLGLTLSNSYWRVSTVHGNVITTNTIFENLWYSCATDSLGVSNCWDFPSMLALSGYVQ"
"GCRALMITAILLGFLGLFLGMVGLRATNVGNMDLSKKAKLLAIAGTLHILAGACGMVAISWYAVNITTDFFNPLYAGTKY"
"ELGPALYLGWSASLLSILGGICVFSTAAASSKEEPATR",
str(hsp.hit.seq),
)
# Check last hit
hit = qresult[num_hits - 1]
self.assertEqual("5YQ7_F", hit.id)
self.assertEqual(
"Beta subunit of light-harvesting 1; Photosynthetic core complex, PHOTOSYNTHESIS; "
"HET: MQE, BCL, HEM, KGD, BPH;{Roseiflexus castenholzii}; Related PDB entries: 5YQ7_V"
" 5YQ7_3 5YQ7_T 5YQ7_J 5YQ7_9 5YQ7_N 5YQ7_A 5YQ7_P 5YQ7_H 5YQ7_D 5YQ7_5 5YQ7_7 5YQ7_1 "
"5YQ7_R",
hit.description,
)
self.assertTrue(hit.is_included)
self.assertEqual(6.7, hit.evalue)
self.assertEqual(20.51, hit.score)
self.assertEqual(1, len(hit))
# Check we can get the original last HSP from the file.
num_hsps = num_hits
self.assertEqual(num_hsps, len(qresult.hsps))
hsp = qresult.hsps[-1]
self.assertTrue(hsp.is_included)
self.assertEqual(num_hsps - 1, hsp.output_index)
self.assertEqual(6.7, hsp.evalue)
self.assertEqual(20.51, hsp.score)
self.assertEqual(52.07, hsp.prob)
self.assertEqual(8, hsp.hit_start)
self.assertEqual(42, hsp.hit_end)
self.assertEqual(5, hsp.query_start)
self.assertEqual(37, hsp.query_end)
self.assertEqual("RTSVVVSTLLGLVMALLIHFVVLSSGAFNWLRAP", str(hsp.hit.seq))
self.assertEqual("SVAVETFGFFMSALGLLMLGLTLSNS--YWRVST", str(hsp.query.seq))
def test_9590198(self):
"""Parsing hhpred_9590198.hhr file."""
txt_file = get_file("hhpred_9590198.hhr")
qresults = parse(txt_file, FMT)
# test first and only qresult
qresult = next(qresults)
num_hits = 22
self.assertEqual("HHSUITE", qresult.program)
self.assertEqual(
"sp|Q9BSU1|CP070_HUMAN UPF0183 protein C16orf70 OS=Homo sapiens OX=9606 GN=C16orf70"
" PE=1 SV=1",
qresult.id,
)
self.assertEqual(422, qresult.seq_len)
self.assertEqual(num_hits, len(qresult))
hit = qresult[0]
self.assertEqual("PF03676.14", hit.id)
self.assertEqual(
"UPF0183 ; Uncharacterised protein family (UPF0183)", hit.description
)
self.assertTrue(hit.is_included)
self.assertEqual(9.9e-102, hit.evalue)
self.assertEqual(792.76, hit.score)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertTrue(hsp.is_included)
self.assertEqual(0, hsp.output_index)
self.assertEqual(9.9e-102, hsp.evalue)
self.assertEqual(792.76, hsp.score)
self.assertEqual(100.00, hsp.prob)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(394, hsp.hit_end)
self.assertEqual(21, hsp.query_start)
self.assertEqual(407, hsp.query_end)
self.assertEqual(
"GMHFSQSVAIIQSQVGTIRGVQVLYSDQNPLSVDLVINMPQDGMRLIFDPVAQRLKIIEIYNMKLVKLRYSGMCFNSPEI"
"TPSIEQVEHCFGATHPGLYDSQRHLFALNFRGLSFYFPVDS-----KFEPGYAHGLGSLQFPNGGSPVVSRTTIYYGSQH"
"QLSSNTSSRVSGVPLPDLPLSCYRQQLHLRRCDVLRNTTSTMGLRLHMFTEGT--SRALEPSQVALVRVVRFGDSCQGVA"
"RALGAPARLYYKADDKMRIHRPTARRR-PPPASDYLFNYFTLGLDVLFDARTNQVKKFVLHTNYPGHYNFNMYHRCEFEL"
"TVQPD-KSEAHSLVESGGGVAVTAYSKWEVVSRAL-RVCERPVVLNRASSTNTTNPFGSTFCYGYQDIIFEVMSNNYIAS"
"ITLY",
str(hsp.hit.seq),
)
self.assertEqual(
"GMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAI"
"APTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQLDSWTEAPKYEPNFAHGLASLQIPHGA--TVKRMYIYSGNSL"
"Q---------DTKA-PMMPLSCFLGNVYAESVDVLRDGTGPAGLRLRLLAAGCGPGLLADAKMRVFERSVYFGDSCQDVL"
"SMLGSPHKVFYKSEDKMKIHSPSPHKQVPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTNYPGHYNFNIYHRCEFKI"
"PLAIKKENADG------QTETCTTYSKWDNIQELLGHPVEKPVVLHRSSSPNNTNPFGSTFCFGLQRMIFEVMQNNHIAS"
"VTLY",
str(hsp.query.seq),
)
# Check last hit
hit = qresult[num_hits - 1]
self.assertEqual("4IL7_A", hit.id)
self.assertEqual(
"Putative uncharacterized protein; partial jelly roll fold, hypothetical; 1.4A "
"{Sulfolobus turreted icosahedral virus}",
hit.description,
)
self.assertTrue(hit.is_included)
self.assertEqual(6.8e02, hit.evalue)
self.assertEqual(22.72, hit.score)
self.assertEqual(1, len(hit))
# Check we can get the original last HSP from the file.
num_hsps = 34
self.assertEqual(num_hsps, len(qresult.hsps))
hsp = qresult.hsps[-1]
self.assertTrue(hsp.is_included)
self.assertEqual(num_hsps - 1, hsp.output_index)
self.assertEqual(3.9e02, hsp.evalue)
self.assertEqual(22.84, hsp.score)
self.assertEqual(21.56, hsp.prob)
self.assertEqual(7, hsp.hit_start)
self.assertEqual(96, hsp.hit_end)
self.assertEqual(18, hsp.query_start)
self.assertEqual(114, hsp.query_end)
self.assertEqual(
"FTLGMPLAQAVAILQKHCRIIKNVQVLYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVH-FN"
"SQAIAPTIEQIDQSFGA",
str(hsp.query.seq),
)
self.assertEqual(
"IQFGMDRTLVWQLAGADQSCSDQVERIICYNNPDH-------YGPQGHFFFNA-ADKLIHKRQMELFPAPKPTMRLATYN"
"KTQTGMTEAQFWAAVPS",
str(hsp.hit.seq),
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)