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
|
#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Tests of parsimony scoring.
"""
import unittest
import dendropy
from dendropy.calculate import treescore
from dendropy.test.support import pathmap
class ParsimonyScoringTest(unittest.TestCase):
def test_pscores_with_standard_data_and_gaps_as_new_states(self):
# #NEXUS
# begin paup;
# set warnroot = no;
# exe apternodus.chars.nexus;
# gett file = apternodus.tre;
# set criterion = parsimony;
# pset gap = newstate;
# pscore;
# end;
expected_scores = [396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 713, 715, 723, 733, 672, 719, 734, 709, 695, 686]
# begin paup;
# set warnroot = no;
# execute apternodus.chars.nexus;
# gett file = apternodus.tre;
# set crit=parsimony;
# pset gap = newstate;
# pscore / single = all scorefile=apternodus.gaps-as-newstate.scores.txt;
# end;
expected_per_site_scores = [
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 4, 2, 1, 2, 3, 4, 5, 5, 3, 4, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 6, 6, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 2, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 3, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 6, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 6, 6, 6, 4, 5, 3, 2, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 2, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 6, 6, 6, 4, 5, 3, 2, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 2, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 6, 6, 6, 4, 5, 3, 2, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 2, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 4, 2, 1, 2, 3, 4, 5, 5, 3, 4, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 6, 6, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 2, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 4, 2, 1, 2, 3, 4, 5, 5, 3, 4, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 6, 6, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 2, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 5, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 6, 6, 4, 5, 3, 2, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 6, 6, 4, 5, 3, 2, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 6, 6, 4, 5, 3, 2, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 3, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 6, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 3, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 6, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 5, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 5, 6, 4, 4, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 6, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 5, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[8, 13, 13, 4, 9, 12, 3, 4, 2, 4, 2, 2, 5, 6, 7, 2, 2, 3, 7, 7, 6, 8, 6, 7, 10, 10, 3, 7, 10, 3, 6, 8, 7, 7, 7, 4, 3, 7, 2, 7, 2, 4, 8, 9, 10, 13, 8, 6, 2, 7, 7, 5, 1, 2, 5, 7, 8, 8, 9, 6, 8, 10, 4, 9, 2, 1, 9, 7, 2, 6, 5, 11, 10, 9, 6, 3, 7, 8, 9, 7, 7, 6, 9, 9, 9, 2, 8, 9, 13, 4, 7, 9, 3, 2, 4, 6, 12, 7, 4, 4, 3, 4, 3, 2, 3, 5, 2, 8, 4, 3, 4, 2, 2, 4, 4, 5, 3, 15,],
[8, 12, 13, 4, 5, 12, 3, 4, 2, 4, 3, 2, 4, 6, 7, 2, 2, 3, 7, 6, 5, 8, 8, 9, 9, 10, 3, 8, 11, 3, 8, 8, 7, 7, 8, 4, 3, 7, 2, 7, 2, 4, 10, 11, 10, 13, 8, 6, 2, 6, 8, 5, 2, 3, 5, 8, 9, 8, 10, 5, 10, 10, 5, 9, 3, 1, 7, 6, 2, 7, 5, 10, 9, 8, 6, 3, 7, 6, 7, 7, 7, 6, 10, 9, 10, 2, 7, 7, 11, 4, 7, 10, 3, 3, 5, 6, 12, 7, 4, 4, 3, 4, 3, 2, 3, 5, 2, 7, 4, 3, 4, 2, 1, 3, 3, 6, 3, 16,],
[7, 12, 11, 4, 10, 10, 3, 4, 2, 4, 3, 2, 5, 7, 8, 2, 2, 3, 7, 5, 8, 10, 9, 9, 10, 8, 3, 9, 11, 3, 7, 6, 8, 8, 9, 4, 3, 7, 2, 6, 2, 4, 9, 7, 10, 12, 8, 6, 2, 6, 9, 5, 2, 3, 5, 7, 9, 10, 9, 5, 8, 11, 5, 9, 3, 1, 10, 6, 2, 7, 5, 11, 10, 9, 6, 3, 7, 8, 7, 7, 6, 6, 10, 7, 9, 2, 8, 8, 14, 4, 7, 10, 3, 3, 5, 7, 14, 6, 3, 4, 3, 4, 1, 2, 3, 5, 2, 6, 4, 3, 4, 2, 2, 5, 4, 5, 2, 14,],
[8, 12, 11, 4, 9, 13, 3, 4, 2, 4, 3, 2, 5, 5, 7, 2, 2, 3, 7, 6, 7, 10, 9, 9, 10, 9, 3, 8, 10, 3, 7, 7, 6, 8, 9, 4, 2, 7, 2, 7, 2, 4, 11, 9, 8, 12, 9, 5, 2, 6, 9, 5, 2, 3, 5, 7, 9, 11, 7, 6, 9, 10, 5, 8, 3, 1, 8, 7, 2, 6, 5, 9, 11, 9, 6, 3, 8, 9, 8, 6, 6, 7, 9, 9, 10, 2, 9, 9, 14, 4, 7, 10, 3, 3, 5, 6, 11, 7, 4, 4, 3, 4, 3, 2, 3, 6, 2, 7, 4, 3, 4, 2, 2, 4, 5, 6, 3, 17,],
[5, 7, 7, 3, 8, 9, 3, 4, 2, 3, 2, 2, 4, 4, 7, 2, 2, 3, 7, 4, 8, 9, 7, 7, 8, 10, 3, 7, 9, 3, 6, 5, 7, 6, 8, 4, 3, 6, 2, 6, 2, 4, 10, 6, 7, 13, 7, 5, 2, 6, 7, 5, 2, 3, 5, 6, 9, 9, 11, 5, 7, 12, 4, 8, 3, 1, 9, 5, 2, 7, 5, 9, 9, 8, 5, 3, 5, 9, 7, 7, 7, 6, 10, 8, 10, 2, 11, 9, 14, 4, 7, 9, 2, 3, 5, 6, 8, 4, 4, 4, 3, 5, 3, 2, 3, 5, 2, 7, 5, 3, 4, 2, 2, 4, 4, 6, 4, 14,],
[7, 11, 12, 4, 8, 13, 3, 4, 2, 4, 3, 2, 5, 7, 8, 2, 2, 3, 7, 5, 5, 8, 9, 9, 10, 9, 3, 9, 10, 3, 8, 6, 9, 6, 8, 4, 3, 6, 2, 6, 2, 4, 9, 9, 9, 12, 8, 5, 2, 7, 9, 4, 2, 3, 5, 10, 9, 9, 9, 6, 10, 9, 5, 9, 3, 1, 10, 8, 2, 7, 5, 10, 9, 10, 6, 3, 7, 7, 7, 7, 7, 7, 8, 8, 8, 2, 7, 9, 13, 4, 7, 9, 3, 3, 5, 7, 14, 6, 4, 4, 3, 3, 3, 2, 3, 5, 2, 6, 3, 3, 4, 2, 2, 4, 5, 2, 4, 15,],
[8, 12, 13, 4, 7, 12, 3, 4, 2, 4, 3, 2, 5, 6, 7, 2, 2, 3, 6, 5, 7, 9, 8, 8, 7, 8, 3, 8, 12, 3, 8, 8, 8, 8, 9, 3, 3, 7, 2, 7, 2, 4, 10, 8, 11, 11, 7, 5, 2, 7, 8, 5, 2, 3, 5, 8, 9, 9, 10, 6, 9, 12, 5, 11, 3, 1, 11, 8, 2, 7, 5, 11, 11, 8, 6, 3, 8, 5, 7, 7, 7, 6, 11, 8, 8, 2, 11, 9, 14, 4, 6, 11, 3, 3, 5, 6, 13, 7, 4, 4, 3, 4, 3, 2, 3, 5, 2, 6, 4, 3, 4, 2, 2, 4, 5, 5, 4, 13,],
[8, 11, 13, 3, 10, 12, 3, 4, 2, 4, 3, 2, 5, 4, 6, 2, 2, 3, 7, 6, 8, 9, 6, 6, 9, 9, 3, 8, 11, 3, 7, 8, 9, 7, 10, 4, 3, 6, 2, 6, 2, 4, 11, 9, 9, 11, 9, 6, 2, 6, 8, 4, 2, 3, 5, 8, 8, 9, 9, 6, 9, 10, 5, 8, 3, 1, 8, 7, 2, 5, 5, 9, 7, 8, 6, 3, 6, 6, 8, 7, 6, 7, 10, 9, 7, 2, 7, 9, 13, 4, 7, 10, 3, 3, 5, 7, 14, 6, 4, 4, 3, 5, 3, 2, 3, 4, 2, 6, 5, 3, 4, 2, 2, 4, 4, 3, 4, 15,],
[6, 12, 11, 4, 9, 11, 3, 3, 2, 4, 3, 2, 3, 6, 7, 2, 2, 3, 6, 6, 9, 10, 9, 9, 10, 10, 3, 9, 11, 3, 7, 7, 6, 8, 7, 4, 3, 6, 1, 5, 2, 3, 9, 7, 8, 9, 8, 5, 2, 7, 8, 5, 2, 3, 5, 8, 9, 11, 8, 6, 8, 10, 5, 8, 3, 1, 6, 6, 2, 6, 5, 11, 8, 11, 6, 3, 8, 8, 7, 7, 7, 5, 9, 9, 10, 2, 7, 9, 11, 4, 7, 8, 3, 2, 4, 7, 13, 5, 4, 4, 2, 4, 2, 2, 2, 4, 2, 5, 4, 3, 4, 2, 2, 6, 5, 4, 3, 13,],
[6, 9, 10, 4, 8, 12, 3, 3, 2, 4, 3, 2, 5, 6, 8, 2, 2, 3, 7, 6, 6, 8, 7, 7, 10, 6, 3, 6, 9, 3, 7, 7, 5, 8, 7, 4, 3, 6, 2, 6, 2, 3, 10, 9, 7, 11, 7, 6, 2, 6, 6, 5, 2, 3, 5, 8, 9, 8, 10, 6, 7, 11, 4, 8, 3, 1, 8, 6, 2, 7, 5, 10, 7, 10, 6, 3, 8, 8, 7, 6, 6, 7, 9, 8, 9, 2, 9, 9, 12, 4, 6, 10, 3, 3, 5, 5, 12, 6, 5, 4, 3, 5, 3, 2, 2, 4, 2, 7, 5, 3, 3, 2, 2, 5, 4, 5, 2, 16,],
]
self.verify_pscores(
trees_fname="apternodus.tre",
chars_fname="apternodus.chars.nexus",
matrix_type=dendropy.StandardCharacterMatrix,
gaps_as_missing=False,
expected_scores=expected_scores,
expected_per_site_scores=expected_per_site_scores)
def test_pscores_with_standard_data_and_gaps_as_missing(self):
# #NEXUS
# begin paup;
# set warnroot = no;
# exe apternodus.chars.nexus;
# gett file = apternodus.tre;
# set criterion = parsimony;
# pset gap = missing;
# pscore;
# end;
expected_scores = [ 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 671, 670, 678, 687, 633, 675, 689, 668, 652, 644]
# begin paup;
# set warnroot = no;
# execute apternodus.chars.nexus;
# gett file = apternodus.tre;
# set crit=parsimony;
# pset gap = missing;
# pscore / single = all scorefile=apternodus.gaps-as-missing.scores.txt;
# end;
expected_per_site_scores = [
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 1, 2, 1, 2, 3, 4, 5, 2, 3, 1, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 5, 5, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 2, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 3, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 5, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 5, 5, 5, 3, 5, 3, 2, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 2, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 5, 5, 5, 3, 5, 3, 2, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 2, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 5, 5, 5, 3, 5, 3, 2, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 2, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 1, 2, 1, 2, 3, 4, 5, 2, 3, 1, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 5, 5, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 2, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 1, 2, 1, 2, 3, 4, 5, 2, 3, 1, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 5, 5, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 2, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 4, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 5, 5, 3, 5, 3, 2, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 5, 5, 3, 5, 3, 2, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 5, 5, 3, 5, 3, 2, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 3, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 5, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 3, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 5, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 4, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 4, 5, 3, 4, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 5, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 4, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,],
[8, 13, 6, 4, 9, 12, 3, 4, 2, 4, 2, 2, 5, 6, 3, 2, 2, 3, 7, 7, 6, 3, 6, 1, 10, 10, 3, 7, 10, 3, 6, 8, 7, 7, 7, 4, 3, 7, 2, 5, 2, 4, 8, 9, 10, 13, 8, 6, 2, 7, 7, 5, 1, 2, 5, 7, 7, 7, 8, 5, 8, 10, 4, 9, 2, 1, 9, 7, 2, 4, 3, 11, 10, 9, 6, 3, 7, 8, 8, 6, 6, 6, 9, 7, 9, 2, 8, 8, 12, 3, 7, 9, 3, 2, 4, 6, 12, 7, 4, 4, 3, 4, 3, 2, 3, 5, 2, 6, 4, 3, 4, 2, 2, 4, 4, 5, 3, 15,],
[8, 12, 5, 4, 5, 12, 3, 4, 2, 4, 3, 2, 4, 6, 3, 2, 2, 3, 7, 6, 5, 3, 8, 1, 9, 10, 3, 8, 11, 3, 8, 8, 7, 7, 8, 4, 3, 7, 2, 5, 2, 4, 10, 11, 10, 13, 8, 6, 2, 6, 8, 5, 2, 3, 5, 8, 8, 7, 9, 4, 10, 10, 5, 9, 3, 1, 7, 6, 2, 5, 3, 10, 9, 8, 6, 3, 7, 6, 6, 6, 6, 6, 10, 7, 10, 2, 7, 6, 10, 3, 7, 10, 3, 3, 5, 6, 12, 7, 4, 4, 3, 4, 3, 2, 3, 5, 2, 5, 4, 3, 4, 2, 1, 3, 3, 6, 3, 16,],
[7, 12, 6, 4, 10, 10, 3, 4, 2, 4, 3, 2, 5, 7, 3, 2, 2, 3, 7, 5, 8, 3, 9, 1, 10, 8, 3, 9, 11, 3, 7, 6, 8, 8, 9, 4, 3, 7, 2, 4, 2, 4, 9, 7, 10, 12, 8, 6, 2, 6, 9, 5, 2, 3, 5, 7, 8, 9, 8, 4, 8, 11, 5, 9, 3, 1, 10, 6, 2, 5, 3, 11, 10, 9, 6, 3, 7, 8, 6, 6, 5, 6, 10, 5, 9, 2, 8, 7, 13, 3, 7, 10, 3, 3, 5, 7, 14, 6, 3, 4, 3, 4, 1, 2, 3, 5, 2, 4, 4, 3, 4, 2, 2, 5, 4, 5, 2, 14,],
[8, 12, 4, 4, 9, 13, 3, 4, 2, 4, 3, 2, 5, 5, 3, 2, 2, 3, 7, 6, 7, 3, 9, 1, 10, 9, 3, 8, 10, 3, 7, 7, 6, 8, 9, 4, 2, 7, 2, 5, 2, 4, 11, 9, 8, 12, 9, 5, 2, 6, 9, 5, 2, 3, 5, 7, 8, 10, 6, 5, 9, 10, 5, 8, 3, 1, 8, 7, 2, 4, 3, 9, 11, 9, 6, 3, 8, 9, 7, 5, 5, 7, 9, 7, 10, 2, 9, 8, 13, 3, 7, 10, 3, 3, 5, 6, 11, 7, 4, 4, 3, 4, 3, 2, 3, 6, 2, 5, 4, 3, 4, 2, 2, 4, 5, 6, 3, 17,],
[5, 7, 4, 3, 8, 9, 3, 4, 2, 3, 2, 2, 4, 4, 3, 2, 2, 3, 7, 4, 8, 3, 7, 1, 8, 10, 3, 7, 9, 3, 6, 5, 7, 6, 8, 4, 3, 6, 2, 4, 2, 4, 10, 6, 7, 13, 7, 5, 2, 6, 7, 5, 2, 3, 5, 6, 8, 8, 10, 4, 7, 12, 4, 8, 3, 1, 9, 5, 2, 5, 3, 9, 9, 8, 5, 3, 5, 9, 6, 6, 6, 6, 10, 6, 10, 2, 11, 8, 13, 3, 7, 9, 2, 3, 5, 6, 8, 4, 4, 4, 3, 5, 3, 2, 3, 5, 2, 5, 5, 3, 4, 2, 2, 4, 4, 6, 4, 14,],
[7, 11, 6, 4, 8, 13, 3, 4, 2, 4, 3, 2, 5, 7, 3, 2, 2, 3, 7, 5, 5, 3, 9, 1, 10, 9, 3, 9, 10, 3, 8, 6, 9, 6, 8, 4, 3, 6, 2, 4, 2, 4, 9, 9, 9, 12, 8, 5, 2, 7, 9, 4, 2, 3, 5, 10, 8, 8, 8, 5, 10, 9, 5, 9, 3, 1, 10, 8, 2, 5, 3, 10, 9, 10, 6, 3, 7, 7, 6, 6, 6, 7, 8, 6, 8, 2, 7, 8, 12, 3, 7, 9, 3, 3, 5, 7, 14, 6, 4, 4, 3, 3, 3, 2, 3, 5, 2, 4, 3, 3, 4, 2, 2, 4, 5, 2, 4, 15,],
[8, 12, 5, 4, 7, 12, 3, 4, 2, 4, 3, 2, 5, 6, 3, 2, 2, 3, 6, 5, 7, 3, 8, 1, 7, 8, 3, 8, 12, 3, 8, 8, 8, 8, 9, 3, 3, 7, 2, 5, 2, 4, 10, 8, 11, 11, 7, 5, 2, 7, 8, 5, 2, 3, 5, 8, 8, 8, 9, 5, 9, 12, 5, 11, 3, 1, 11, 8, 2, 5, 3, 11, 11, 8, 6, 3, 8, 5, 6, 6, 6, 6, 11, 6, 8, 2, 11, 8, 13, 3, 6, 11, 3, 3, 5, 6, 13, 7, 4, 4, 3, 4, 3, 2, 3, 5, 2, 4, 4, 3, 4, 2, 2, 4, 5, 5, 4, 13,],
[8, 11, 5, 3, 10, 12, 3, 4, 2, 4, 3, 2, 5, 4, 3, 2, 2, 3, 7, 6, 8, 3, 6, 1, 9, 9, 3, 8, 11, 3, 7, 8, 9, 7, 10, 4, 3, 6, 2, 5, 2, 4, 11, 9, 9, 11, 9, 6, 2, 6, 8, 4, 2, 3, 5, 8, 7, 8, 8, 5, 9, 10, 5, 8, 3, 1, 8, 7, 2, 3, 3, 9, 7, 8, 6, 3, 6, 6, 7, 6, 5, 7, 10, 7, 7, 2, 7, 8, 12, 3, 7, 10, 3, 3, 5, 7, 14, 6, 4, 4, 3, 5, 3, 2, 3, 4, 2, 4, 5, 3, 4, 2, 2, 4, 4, 3, 4, 15,],
[6, 12, 5, 4, 9, 11, 3, 3, 2, 4, 3, 2, 3, 6, 3, 2, 2, 3, 6, 6, 9, 3, 9, 1, 10, 10, 3, 9, 11, 3, 7, 7, 6, 8, 7, 4, 3, 6, 1, 4, 2, 3, 9, 7, 8, 9, 8, 5, 2, 7, 8, 5, 2, 3, 5, 8, 8, 10, 7, 5, 8, 10, 5, 8, 3, 1, 6, 6, 2, 4, 3, 11, 8, 11, 6, 3, 8, 8, 6, 6, 6, 5, 9, 7, 10, 2, 7, 8, 10, 3, 7, 8, 3, 2, 4, 7, 13, 5, 4, 4, 2, 4, 2, 2, 2, 4, 2, 4, 4, 3, 4, 2, 2, 6, 5, 4, 3, 13,],
[6, 9, 4, 4, 8, 12, 3, 3, 2, 4, 3, 2, 5, 6, 3, 2, 2, 3, 7, 6, 6, 3, 7, 1, 10, 6, 3, 6, 9, 3, 7, 7, 5, 8, 7, 4, 3, 6, 2, 4, 2, 3, 10, 9, 7, 11, 7, 6, 2, 6, 6, 5, 2, 3, 5, 8, 8, 7, 9, 5, 7, 11, 4, 8, 3, 1, 8, 6, 2, 5, 3, 10, 7, 10, 6, 3, 8, 8, 6, 5, 5, 7, 9, 6, 9, 2, 9, 8, 11, 3, 6, 10, 3, 3, 5, 5, 12, 6, 5, 4, 3, 5, 3, 2, 2, 4, 2, 5, 5, 3, 3, 2, 2, 5, 4, 5, 2, 16,],
]
self.verify_pscores(
trees_fname="apternodus.tre",
chars_fname="apternodus.chars.nexus",
matrix_type=dendropy.StandardCharacterMatrix,
gaps_as_missing=True,
expected_scores=expected_scores,
expected_per_site_scores=expected_per_site_scores)
def test_pscores_with_dna_data_and_gaps_as_new_states(self):
# #NEXUS
# begin paup;
# set warnroot = no;
# exe apternodus.chars.nexus;
# gett file = apternodus.tre;
# set criterion = parsimony;
# pset gap = newstate;
# pscore;
# end;
expected_scores = [4703]
# begin paup;
# set warnroot = no;
# execute pythonindae.chars.nexus;
# gett file = pythonidae.mle.tre;
# set crit=parsimony;
# pset gap = newstate;
# pscore / single = all scorefile=pythonidae.gaps-as-newstate.scores.txt;
# end;
expected_per_site_scores = [
[0, 6, 5, 3, 3, 3, 6, 4, 2, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 4, 11, 7,
2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 2, 3, 5, 10, 3,
6, 0, 0, 1, 3, 1, 1, 3, 1, 3, 2, 4, 4, 4, 8, 7, 7, 5, 3, 2, 2,
2, 5, 1, 0, 4, 3, 2, 2, 4, 5, 3, 6, 5, 7, 3, 10, 1, 2, 5, 10,
4, 1, 6, 2, 8, 5, 5, 5, 1, 7, 2, 3, 5, 2, 2, 1, 7, 11, 3, 4, 3,
2, 1, 1, 2, 1, 4, 10, 6, 10, 4, 10, 8, 7, 9, 11, 7, 5, 8, 3, 3,
4, 9, 7, 5, 2, 3, 3, 5, 4, 4, 3, 3, 5, 1, 5, 1, 1, 0, 4, 0, 0,
0, 0, 0, 0, 0, 0, 4, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 8, 1, 4, 9,
8, 7, 9, 4, 3, 6, 8, 1, 2, 2, 7, 9, 7, 9, 5, 6, 1, 1, 1, 1, 1,
2, 4, 9, 4, 5, 3, 6, 6, 6, 5, 10, 7, 9, 4, 7, 10, 13, 8, 4, 5,
8, 9, 10, 12, 7, 9, 7, 6, 8, 8, 7, 5, 6, 6, 4, 7, 9, 8, 8, 8,
6, 7, 2, 2, 6, 5, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 2, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 1, 3, 1, 0, 0, 0, 0, 2, 0, 0, 0, 0, 3,
0, 0, 0, 4, 0, 1, 0, 2, 0, 4, 2, 0, 1, 0, 0, 0, 7, 0, 2, 4, 1,
1, 5, 3, 0, 1, 0, 0, 0, 0, 0, 1, 0, 3, 4, 0, 0, 1, 1, 1, 6, 4,
8, 1, 0, 1, 2, 1, 10, 3, 0, 0, 0, 4, 10, 5, 3, 5, 2, 5, 4, 9,
9, 2, 4, 1, 1, 1, 7, 0, 0, 2, 0, 0, 0, 1, 5, 7, 7, 4, 2, 1, 0,
0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 1, 1, 2, 2, 3, 11, 0, 1, 4, 4, 1,
2, 3, 1, 3, 2, 9, 7, 1, 3, 0, 5, 0, 0, 1, 2, 6, 2, 5, 2, 6, 1,
0, 0, 0, 8, 6, 0, 0, 0, 2, 0, 1, 1, 3, 4, 3, 1, 1, 0, 2, 1, 3,
1, 6, 0, 0, 3, 1, 1, 5, 0, 3, 1, 4, 8, 4, 6, 0, 3, 6, 3, 5, 2,
1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 1, 3, 0, 3, 4, 3, 3, 2, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0,
1, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 3, 3, 8,
4, 2, 0, 3, 5, 2, 1, 3, 2, 0, 0, 0, 0, 4, 3, 2, 3, 7, 5, 5, 0,
2, 3, 4, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 2, 2, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 2, 0,
2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 1, 1,
0, 3, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 4, 0, 0, 0, 0, 0, 2, 0, 0,
0, 1, 2, 0, 0, 5, 5, 2, 7, 7, 4, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0,
0, 1, 0, 0, 0, 7, 3, 0, 0, 0, 0, 4, 6, 3, 5, 4, 1, 0, 2, 3, 0,
0, 2, 3, 0, 0, 0, 0, 7, 5, 1, 5, 1, 0, 2, 0, 0, 0, 0, 5, 2, 1,
0, 1, 4, 1, 3, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 3, 1, 0,
0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 0, 0, 7,
1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 4, 1, 0, 3, 2, 0, 6, 4, 0,
0, 0, 1, 2, 7, 0, 3, 0, 0, 5, 0, 0, 3, 0, 0, 5, 2, 0, 4, 0, 0,
6, 0, 0, 0, 0, 0, 2, 0, 0, 3, 0, 0, 3, 0, 0, 4, 0, 0, 1, 0, 0,
2, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 5, 0, 0, 3, 1, 0,
0, 6, 0, 0, 6, 0, 1, 1, 0, 3, 0, 0, 11, 8, 1, 4, 2, 5, 8, 7, 0,
2, 0, 0, 1, 2, 1, 3, 10, 1, 3, 0, 0, 6, 0, 0, 7, 0, 0, 3, 0, 2,
5, 5, 0, 5, 1, 0, 11, 1, 0, 8, 0, 0, 4, 0, 0, 4, 0, 0, 1, 0, 0,
2, 0, 0, 4, 0, 0, 11, 1, 0, 3, 1, 0, 6, 0, 0, 0, 0, 0, 8, 0, 1,
2, 0, 0, 3, 0, 0, 7, 6, 0, 12, 0, 0, 3, 0, 0, 9, 2, 1, 3, 0, 0,
4, 1, 0, 6, 0, 0, 2, 0, 0, 2, 2, 1, 7, 0, 0, 5, 0, 0, 2, 2, 1,
2, 1, 0, 0, 0, 0, 1, 0, 0, 2, 4, 0, 9, 0, 0, 3, 0, 0, 8, 0, 0,
1, 0, 0, 1, 0, 0, 1, 0, 0, 9, 2, 0, 0, 0, 0, 3, 0, 0, 5, 0, 0,
10, 0, 0, 5, 1, 0, 10, 0, 0, 4, 0, 0, 11, 1, 0, 5, 0, 0, 7, 0,
0, 2, 0, 0, 6, 0, 0, 7, 4, 0, 3, 0, 0, 1, 0, 0, 6, 0, 0, 6, 0,
0, 10, 1, 0, 3, 2, 0, 13, 0, 0, 4, 0, 0, 0, 0, 0, 2, 0, 0, 5,
0, 0, 2, 1, 0, 1, 0, 0, 12, 0, 0, 11, 0, 1, 11, 0, 0, 3, 1, 0,
12, 0, 0, 6, 0, 0, 5, 0, 3, 2, 5, 0, 5, 0, 0, 3, 0, 0, 6, 0, 0, 7,
0, 0, 7, 0, 0, 2, 0, 0, 5, 0, 0, 8, 0, 0, 9, 0, 0, 10, 0, 0, 6, 1,
0, 1, 0, 0, 3, 0, 0, 2, 0, 0, 4, 0, 0, 3, 0, 0, 1, 0, 0, 1, 0, 0,
1, 0, 0, 4, 0, 0, 1, 0, 0, 8, 0, 0, 2, 0, 0, 9, 0, 0, 3, 0, 0, 4,
1, 0, 3, 2, 0, 9, 0, 0, 7, 0, 0, 8, 3, 0, 6, 0, 0, 10, 0, 0, 3, 2,
0, 7, 0, 0, 7, 1, 0, 1, 2, 0, 8, 5, 0, 4, 0, 0, 2, 0, 0, 6, 0, 0,
6, 7, 0, 9, 0, 0, 4, 0, 0, 7, 0, 0, 10, 0, 0, 6, 0, 0, 1, 0, 0, 2,
0, 0, 9, 0, 0, 6, 0, 0, 10, 0, 0, 5, 3, 0, 9, 0, 0, 4, 0, 0, 3, 0,
0, 5, 0, 0, 7, 0, 0, 4, 3, 0, 2, 0, 0, 3, 0, 0, 4, 0, 0, 6, 3, 0,
3, 0, 0, 2, 0, 0, 1, 2, 4, 4, 0, 0, 8, 0, 0, 6, 0, 0, 10, 11, 0, 4,
0, 0, 5, 0, 0, 1, 5, 0, 2, 0, 0, 3, 7, 0, 5, 0, 0, 8, 6, 0, 6, 0,
0, 12, 0, 0, 6, 0, 0, 3, 0, 0, 5, 0, 0, 10, 0, 0, 10, 1, 0, 1, 0,
0, 4, 0, 0, 3, 7, 0, 1, 0, 0, 3, 0, 0, 7, 0, 0, 3, 1, 0, 3, 0, 0,
2, 0, 0, 5, 0, 0, 5, 0, 0, 0, 0, 0, 3, 0, 0, 3, 0, 0, 2, 0, 0, 4,
0, 0, 14, 0, 0, 7, 0, 0, 1, 5, 0, 7, 7, 0, 2, 0, 0, 0, 0, 0, 6, 5,
0, 12, 1, 0, 8, 7, 0, 3, 5, 0, 5, 1, 1, 3, 4, 0, 4, 1, 0, 1, 5, 3,
9, 7, 1, 7, 7, 9, 9, 8, 0, 2, 7, 0, 7, 1, 1, 9, 2, 3, 5, 5, 2, 9,
0, 1, 6, 0, 0, 3, 2, 1, 3, 0, 0, 5, 1, 0, 8, 0, 0, 11, 1, 0, 9, 1,
0, 8, 0, 0, 2, 0, 0, 2, 0, 0, 6, 0, 0, 4, 0, 0, 1, 0, 0, 1, 0, 0,
0, 0, 0, 8, 0, 0, 4, 0, 0, 11, 7, 0, 4, 0, 0, 5, 0, 0, 2, 0, 0, 2,
0, 0, 4, 0, 0, 2, 0, 0, 8, 0, 0, 0, 0, 0, 1, 0, 0, 10, 0, 1, 8, 0,
0, 3, 0, 0, 4, 2, 0, 2, 0, 0, 7, 0, 0, 2, 0, 0, 9, 0, 0, 11, 0, 0,
8, 1, 0, 1, 0, 0, 1, 0, 0, 9, 0, 0, 6, 0, 1, 5, 0, 0, 8, 1, 0, 2,
2, 0, 9, 0, 0, 4, 0, 0, 7, 0, 0, 4, 8, 0, 1, 0, 0, 6, 6, 0, 1, 2,
1, 2, 1, 1, 0, 1, 0, 7, 0, 0, 6, 1, 0, 1, 0, 0, 8, 6, 0, 1, 2, 0,
10, 2, 3, 8, 3, 6, 5, 0, 0, 2, 1, 0, 6, 0, 4, 0, 0, 0, 4, 0, 0, 1,
2, 0, 3, 8, 5, 8, 4, 0, 10, 0, 0, 7, 2, 0, 11, 1, 0, 0, 0, 0, 6, 0,
0, 3, 0, 0, 7, 0, 0, 8, 5, 0, 10, 2, 2, 2, 0, 0, 0, 4, 0, 6, 0, 2,
2, 0, 0, 8, 0, 0, 0, 2, 1, 1, 7, 0, 2, 9, 0, 12, 3, 0, 2, 0, 0, 1,
0, 0, 7, 4, 6, 3, 0, 1, 6, 0, 0, 8, 0, 0, 1, 0, 0, 6, 1, 1, 5, 0,
0, 1, 0, 1, 0, 0, 0, 2, 0, 0, 5, 0, 0, 0, 0, 0, 2, 0, 0, 8, 0, 0,
1, 0, 5, 9, 0, 1, 8, 7, 8, 8, 0, 0, 9, 0, 0, 3, 0, 0, 1, 3, 9, 2,
1, 0, 10, 4, 0, 0, 5, 3, 5, 4, 1, 4, 0, 0, 4, 0, 0, 2, 1, 2, 4, 0,
1, 3, 0, 0, 5, 6, 1, 5, 3, 1, 9, 1, 7, 3, 0, 0, 7, 5, 0, 9, 4, 2,
6, 0, 0, 10, 0, 0, 5, 8, 4, 7, 0, 0, 1, 0, 0, 7, 0, 0, 0, 0, 0, 2,
0, 2, 0, 2, 0, 6, 4, 7, 6, 7, 4, 6, 0, 2, 1, 6, 3, 3, 3, 0, 0, 7,
5, 3, 1, 0, 5, 8, 3, 5, 3, 2, 8, 8, 2, 8, 10, 7, 1, 1, 0, 0, 1, 1,
1, 1, 0, 0, 0, 0, 0, 0, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 2, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 3, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 3, 0, 0, 1, 1, 0, 0, 0,
1, 1, 2, 1, 0, 5, 0, 0, 0, 3, 10, 7, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 2, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0,
0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 2, 2, 0, 5, 2,
1, 0, 8, 0, 0, 1, 6, 8, 3, 3, 2, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 1, 6, 0, 0, 0, 1,
2, 1, 0, 0, 0, 3, 2, 7, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1, 1, 3, 3, 0, 0, 0, 2, 6, 0, 6, 0, 0, 2, 0, 0,
3, 0, 0, 2, 1, 3, 5, 2, 0, 0, 0, 0, 0, 7, 9, 8, 6, 1, 3, 2, 3, 5,
6, 0, 0, 0, 0, 4, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 2,
2, 2, 3, 0, 4, 0, 0, 0, 5, 0, 0, 3, 1, 0, 2, 2, 0, 3, 0, 0, 0, 0,
1, 0, 2, 2, 2, 3, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 3, 1, 5, 3, 1, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 2,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 1, 0, 0, 0, 0, 2, 0, 0, 2,
1, 2, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 10, 1, 1, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 5, 3, 1, 0, 0, 0, 1,
0, 0, 0, 0, 1, 0, 0, 1, 1, 3, 8, 1, 1, 1, 8, 9, 5, 3, 1, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 1, 3, 0, 1, 2, 3, 0, 1, 1, 1, 2, 1, 0, 0, 0, 1, 0,
12, 8, 7, 0, 0, 0, 1, 0, 9, 5, 2, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 4,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5, 0, 2, 7, 1, 1, 2, 0, 3, 3, 11, 4,
0, 10, 3, 0, 1, 0, 1, 1, 3, 2, 9, 5, 6, 10, 2, 1, 0, 0, 1, 1, 1, 1,
0, 0, 0, 0, 1, 0, 0, 0, 5, 7, 1, 7, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
1, 1, 8, 0, 0, 0, 0, 0, 6, 2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0,
0, 0, 0, 0, 0, 0, 0, 7, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 3, 3, 1, 0,
0, 0, 4, 0, 0, 0, 1, 2, 1, 0, 0, 0, 0, 0, 3, 0, 0, 1, 0, 0, 0, 1,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 0,],
]
self.verify_pscores(
trees_fname="pythonidae.mle.nex",
chars_fname="pythonidae.chars.nexus",
matrix_type=dendropy.DnaCharacterMatrix,
gaps_as_missing=False,
expected_scores=expected_scores,
expected_per_site_scores=expected_per_site_scores)
def test_pscores_with_dna_data_and_gaps_as_missing(self):
# #NEXUS
# begin paup;
# set warnroot = no;
# exe apternodus.chars.nexus;
# gett file = apternodus.tre;
# set criterion = parsimony;
# pset gap = newstate;
# pscore;
# end;
expected_scores = [4271]
# begin paup;
# set warnroot = no;
# execute pythonindae.chars.nexus;
# gett file = pythonidae.mle.tre;
# set crit=parsimony;
# pset gap = missing;
# pscore / single = all scorefile=pythonidae.gaps-as-newstate.scores.txt;
# end;
expected_per_site_scores = [
[0, 6, 3, 3, 3, 2, 4, 3, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 6, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 2, 8, 2,
4, 0, 0, 1, 3, 0, 0, 2, 0, 2, 1, 3, 3, 1, 2, 2, 2, 2, 2, 1, 0,
1, 5, 1, 0, 4, 3, 2, 2, 4, 2, 0, 4, 5, 7, 3, 10, 1, 2, 5, 10,
4, 1, 6, 1, 6, 3, 2, 4, 1, 7, 2, 3, 5, 2, 0, 0, 6, 10, 2, 3, 3,
2, 0, 0, 1, 0, 3, 7, 3, 7, 2, 6, 6, 4, 5, 8, 4, 2, 6, 0, 0, 1,
4, 3, 2, 0, 1, 1, 1, 1, 1, 2, 3, 4, 1, 1, 1, 0, 0, 4, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 8, 7,
7, 9, 4, 1, 3, 6, 0, 2, 2, 7, 9, 7, 8, 4, 2, 0, 0, 0, 0, 0, 0,
4, 9, 4, 5, 3, 4, 3, 4, 3, 7, 5, 7, 2, 5, 7, 11, 5, 3, 4, 5, 8,
9, 11, 6, 8, 7, 6, 8, 8, 7, 5, 6, 6, 4, 6, 8, 7, 7, 6, 4, 3, 1,
1, 5, 5, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 1, 3, 1, 0, 0, 0, 0, 2, 0, 0, 0, 0, 3, 0, 0, 0,
4, 0, 1, 0, 2, 0, 4, 2, 0, 1, 0, 0, 0, 7, 0, 2, 4, 1, 1, 5, 3,
0, 1, 0, 0, 0, 0, 0, 1, 0, 3, 4, 0, 0, 1, 1, 1, 6, 4, 7, 1, 0,
1, 2, 1, 10, 1, 0, 0, 0, 4, 10, 5, 3, 5, 2, 5, 4, 8, 9, 2, 3,
0, 0, 0, 5, 0, 0, 2, 0, 0, 0, 1, 5, 7, 6, 2, 2, 1, 0, 0, 0, 0,
0, 0, 1, 2, 0, 0, 0, 1, 1, 2, 2, 3, 11, 0, 1, 4, 4, 0, 0, 0, 0,
3, 2, 9, 6, 0, 3, 0, 5, 0, 0, 0, 2, 6, 2, 5, 2, 6, 1, 0, 0, 0,
8, 6, 0, 0, 0, 2, 0, 0, 0, 3, 4, 3, 1, 0, 0, 2, 1, 3, 1, 6, 0,
0, 3, 0, 1, 5, 0, 3, 1, 4, 8, 4, 6, 0, 3, 6, 3, 5, 0, 0, 1, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
3, 0, 3, 4, 3, 2, 2, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1,
1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 3, 3, 8, 4, 0, 0,
3, 5, 2, 0, 3, 2, 0, 0, 0, 0, 4, 3, 1, 3, 7, 5, 3, 0, 2, 3, 4,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 2, 2, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 2, 0, 2, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 1, 1, 0, 3, 0,
0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 4, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 2,
0, 0, 5, 4, 2, 7, 7, 4, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0,
0, 0, 7, 3, 0, 0, 0, 0, 4, 6, 3, 5, 4, 0, 0, 2, 3, 0, 0, 2, 3,
0, 0, 0, 0, 7, 5, 1, 5, 1, 0, 2, 0, 0, 0, 0, 0, 0, 1, 0, 1, 3,
0, 3, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 3, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 1, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 4, 1, 0, 3, 2, 0, 6, 4, 0, 0, 0, 1,
2, 7, 0, 3, 0, 0, 5, 0, 0, 3, 0, 0, 5, 2, 0, 4, 0, 0, 6, 0, 0,
0, 0, 0, 2, 0, 0, 3, 0, 0, 3, 0, 0, 4, 0, 0, 1, 0, 0, 2, 0, 0,
0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 5, 0, 0, 3, 1, 0, 0, 6, 0,
0, 6, 0, 1, 1, 0, 3, 0, 0, 11, 8, 1, 4, 2, 5, 8, 7, 0, 2, 0, 0,
1, 2, 1, 3, 10, 1, 3, 0, 0, 6, 0, 0, 7, 0, 0, 3, 0, 2, 5, 5, 0,
5, 1, 0, 11, 1, 0, 8, 0, 0, 4, 0, 0, 4, 0, 0, 1, 0, 0, 2, 0, 0,
4, 0, 0, 11, 1, 0, 3, 1, 0, 6, 0, 0, 0, 0, 0, 8, 0, 1, 2, 0, 0,
3, 0, 0, 7, 6, 0, 12, 0, 0, 3, 0, 0, 9, 2, 1, 3, 0, 0, 4, 1, 0,
6, 0, 0, 2, 0, 0, 2, 2, 1, 7, 0, 0, 5, 0, 0, 1, 2, 1, 2, 1, 0,
0, 0, 0, 1, 0, 0, 2, 4, 0, 9, 0, 0, 3, 0, 0, 8, 0, 0, 1, 0, 0,
1, 0, 0, 1, 0, 0, 9, 2, 0, 0, 0, 0, 3, 0, 0, 5, 0, 0, 10, 0, 0,
5, 1, 0, 10, 0, 0, 4, 0, 0, 11, 1, 0, 5, 0, 0, 7, 0, 0, 2, 0,
0, 6, 0, 0, 7, 4, 0, 3, 0, 0, 1, 0, 0, 6, 0, 0, 6, 0, 0, 10, 1,
0, 3, 2, 0, 13, 0, 0, 4, 0, 0, 0, 0, 0, 2, 0, 0, 5, 0, 0, 2, 1,
0, 1, 0, 0, 12, 0, 0, 11, 0, 1, 11, 0, 0, 3, 1, 0, 12, 0, 0, 6,
0, 0, 5, 0, 3, 2, 5, 0, 5, 0, 0, 3, 0, 0, 6, 0, 0, 7, 0, 0, 7, 0,
0, 2, 0, 0, 5, 0, 0, 8, 0, 0, 9, 0, 0, 10, 0, 0, 6, 1, 0, 1, 0, 0,
3, 0, 0, 2, 0, 0, 4, 0, 0, 3, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 4,
0, 0, 1, 0, 0, 8, 0, 0, 2, 0, 0, 9, 0, 0, 3, 0, 0, 4, 1, 0, 3, 2,
0, 9, 0, 0, 7, 0, 0, 8, 3, 0, 6, 0, 0, 10, 0, 0, 3, 2, 0, 7, 0, 0,
7, 1, 0, 1, 2, 0, 8, 5, 0, 4, 0, 0, 2, 0, 0, 6, 0, 0, 6, 7, 0, 9,
0, 0, 4, 0, 0, 7, 0, 0, 10, 0, 0, 6, 0, 0, 1, 0, 0, 2, 0, 0, 9, 0,
0, 6, 0, 0, 10, 0, 0, 5, 3, 0, 9, 0, 0, 4, 0, 0, 3, 0, 0, 5, 0, 0,
7, 0, 0, 4, 3, 0, 2, 0, 0, 3, 0, 0, 4, 0, 0, 6, 3, 0, 3, 0, 0, 2,
0, 0, 1, 2, 4, 4, 0, 0, 8, 0, 0, 6, 0, 0, 10, 11, 0, 4, 0, 0, 5, 0,
0, 1, 5, 0, 2, 0, 0, 3, 7, 0, 5, 0, 0, 8, 6, 0, 6, 0, 0, 12, 0, 0,
6, 0, 0, 3, 0, 0, 5, 0, 0, 10, 0, 0, 10, 1, 0, 1, 0, 0, 4, 0, 0, 3,
7, 0, 1, 0, 0, 3, 0, 0, 7, 0, 0, 3, 1, 0, 3, 0, 0, 2, 0, 0, 5, 0,
0, 5, 0, 0, 0, 0, 0, 3, 0, 0, 3, 0, 0, 2, 0, 0, 4, 0, 0, 14, 0, 0,
7, 0, 0, 1, 5, 0, 7, 7, 0, 2, 0, 0, 0, 0, 0, 6, 5, 0, 12, 1, 0, 8,
7, 0, 3, 5, 0, 5, 1, 1, 3, 4, 0, 4, 1, 0, 1, 5, 3, 9, 7, 1, 7, 7,
9, 9, 8, 0, 2, 7, 0, 7, 1, 1, 9, 2, 3, 5, 5, 2, 9, 0, 1, 6, 0, 0,
3, 2, 1, 3, 0, 0, 5, 1, 0, 8, 0, 0, 11, 1, 0, 9, 1, 0, 8, 0, 0, 2,
0, 0, 2, 0, 0, 6, 0, 0, 4, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 8, 0,
0, 4, 0, 0, 11, 7, 0, 4, 0, 0, 5, 0, 0, 2, 0, 0, 2, 0, 0, 4, 0, 0,
2, 0, 0, 8, 0, 0, 0, 0, 0, 1, 0, 0, 10, 0, 1, 8, 0, 0, 3, 0, 0, 4,
2, 0, 2, 0, 0, 7, 0, 0, 2, 0, 0, 9, 0, 0, 11, 0, 0, 8, 1, 0, 1, 0,
0, 1, 0, 0, 9, 0, 0, 6, 0, 1, 5, 0, 0, 8, 1, 0, 2, 2, 0, 9, 0, 0,
4, 0, 0, 7, 0, 0, 4, 8, 0, 1, 0, 0, 6, 6, 0, 1, 2, 1, 2, 1, 1, 0,
1, 0, 7, 0, 0, 6, 1, 0, 1, 0, 0, 8, 6, 0, 1, 2, 0, 10, 2, 3, 8, 3,
6, 5, 0, 0, 2, 1, 0, 6, 0, 4, 0, 0, 0, 4, 0, 0, 1, 2, 0, 3, 8, 5,
8, 4, 0, 10, 0, 0, 7, 2, 0, 11, 1, 0, 0, 0, 0, 6, 0, 0, 3, 0, 0, 7,
0, 0, 8, 5, 0, 10, 2, 2, 2, 0, 0, 0, 4, 0, 6, 0, 2, 2, 0, 0, 8, 0,
0, 0, 2, 1, 1, 7, 0, 2, 9, 0, 12, 3, 0, 2, 0, 0, 1, 0, 0, 7, 4, 6,
3, 0, 1, 6, 0, 0, 8, 0, 0, 1, 0, 0, 6, 1, 1, 5, 0, 0, 1, 0, 1, 0,
0, 0, 2, 0, 0, 5, 0, 0, 0, 0, 0, 2, 0, 0, 8, 0, 0, 1, 0, 5, 9, 0,
1, 8, 7, 8, 8, 0, 0, 9, 0, 0, 3, 0, 0, 1, 3, 9, 2, 1, 0, 10, 4, 0,
0, 5, 3, 5, 4, 1, 4, 0, 0, 4, 0, 0, 2, 1, 2, 4, 0, 1, 3, 0, 0, 5,
6, 1, 5, 3, 1, 9, 1, 7, 3, 0, 0, 7, 5, 0, 9, 4, 2, 6, 0, 0, 10, 0,
0, 5, 8, 4, 7, 0, 0, 1, 0, 0, 7, 0, 0, 0, 0, 0, 2, 0, 2, 0, 2, 0,
6, 4, 7, 6, 7, 4, 6, 0, 2, 1, 5, 3, 3, 3, 0, 0, 7, 5, 3, 1, 0, 5,
8, 3, 5, 3, 2, 6, 2, 0, 1, 5, 6, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 2, 0, 3, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0,
0, 0, 0, 0, 1, 0, 1, 0, 0, 3, 0, 0, 1, 1, 0, 0, 0, 1, 1, 2, 1, 0,
5, 0, 0, 0, 3, 8, 7, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0,
0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 1,
0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 2, 2, 0, 5, 2, 1, 0, 8, 0, 0,
0, 6, 8, 3, 2, 1, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 1, 6, 0, 0, 0, 1, 2, 1, 0, 0, 0,
3, 2, 7, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 1, 3, 3, 0, 0, 0, 2, 6, 0, 6, 0, 0, 2, 0, 0, 3, 0, 0, 2, 1,
3, 5, 2, 0, 0, 0, 0, 0, 7, 9, 8, 6, 1, 3, 2, 3, 5, 6, 0, 0, 0, 0,
4, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 2, 2, 2, 3, 0, 4,
0, 0, 0, 5, 0, 0, 3, 1, 0, 2, 2, 0, 3, 0, 0, 0, 0, 1, 0, 2, 1, 1,
3, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 3, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 3, 0, 5, 3, 1, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 2, 0, 1, 0, 0, 0, 0, 2, 0, 0, 2, 1, 2, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 10, 1, 1, 0, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 5, 3, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1,
0, 0, 1, 1, 3, 8, 1, 1, 1, 8, 9, 5, 3, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
1, 3, 0, 1, 2, 3, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 12, 8, 7, 0, 0,
0, 1, 0, 9, 5, 2, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 4, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 5, 0, 2, 5, 1, 1, 2, 0, 3, 3, 11, 4, 0, 10, 3, 0, 0,
0, 1, 1, 3, 2, 9, 5, 6, 8, 1, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1,
0, 0, 0, 5, 7, 1, 7, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 8, 0, 0,
0, 0, 0, 6, 2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0,
0, 0, 7, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 3, 3, 1, 0, 0, 0, 4, 0, 0,
0, 1, 2, 1, 0, 0, 0, 0, 0, 3, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,]
]
self.verify_pscores(
trees_fname="pythonidae.mle.nex",
chars_fname="pythonidae.chars.nexus",
matrix_type=dendropy.DnaCharacterMatrix,
gaps_as_missing=True,
expected_scores=expected_scores,
expected_per_site_scores=expected_per_site_scores)
def verify_pscores(self,
trees_fname,
chars_fname,
matrix_type,
gaps_as_missing,
expected_scores,
expected_per_site_scores):
taxon_namespace = dendropy.TaxonNamespace()
chars = matrix_type.get(
path=pathmap.char_source_path(chars_fname),
schema="nexus",
taxon_namespace=taxon_namespace)
trees = dendropy.TreeList.get(
path=pathmap.tree_source_path(trees_fname),
schema="nexus",
taxon_namespace=taxon_namespace)
self.assertEqual(len(expected_scores), len(trees))
for tree_idx, tree in enumerate(trees):
score_by_character_list = []
pscore = treescore.parsimony_score(
tree,
chars,
gaps_as_missing=gaps_as_missing,
score_by_character_list=score_by_character_list)
self.assertEqual(pscore, expected_scores[tree_idx])
self.assertEqual(len(score_by_character_list), len(expected_per_site_scores[tree_idx]))
for obs, exp in zip(score_by_character_list, expected_per_site_scores[tree_idx]):
self.assertEqual(obs, exp)
self.assertEqual(sum(score_by_character_list), pscore)
# just to be sure it works without passing in `score_by_character_list`:
pscore = treescore.parsimony_score(
tree,
chars,
gaps_as_missing=gaps_as_missing)
self.assertEqual(pscore, expected_scores[tree_idx])
if __name__ == "__main__":
unittest.main()
|
