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comparison clipkit_repo/tests/unit/test_modes.py @ 0:49b058e85902 draft

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"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author padge
date Fri, 25 Mar 2022 13:04:31 +0000
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-1:000000000000 0:49b058e85902
1 import pytest
2 from pathlib import Path
3
4 import numpy as np
5 from Bio import AlignIO
6 from clipkit.modes import TrimmingMode, trim, shouldKeep
7
8 here = Path(__file__)
9
10
11 class TestModes(object):
12 def test_shouldKeep_kpi_gappy_keep(self):
13 ## setup
14 mode = TrimmingMode.kpi_gappy
15 gappyness = 0.00
16 gaps = 0.9
17 parsimony_informative = True
18 constant_site = False
19
20 assert True == shouldKeep(
21 mode, parsimony_informative, constant_site, gappyness, gaps
22 )
23
24 def test_shouldKeep_kpi_gappy_trim(self):
25 ## setup
26 mode = TrimmingMode.kpi_gappy
27 gappyness = 0.00
28 gaps = 0.9
29 parsimony_informative = False
30 constant_site = False
31
32 assert False == shouldKeep(
33 mode, parsimony_informative, constant_site, gappyness, gaps
34 )
35
36 def test_shouldKeep_gappy_keep(self):
37 ## setup
38 mode = TrimmingMode.gappy
39 gappyness = 0.00
40 gaps = 0.9
41 parsimony_informative = True
42 constant_site = False
43
44 assert True == shouldKeep(
45 mode, parsimony_informative, constant_site, gappyness, gaps
46 )
47
48 def test_shouldKeep_gappy_trim(self):
49 ## setup
50 mode = TrimmingMode.gappy
51 gappyness = 0.95
52 gaps = 0.9
53 parsimony_informative = True
54 constant_site = False
55
56 assert False == shouldKeep(
57 mode, parsimony_informative, constant_site, gappyness, gaps
58 )
59
60 def test_shouldKeep_kpi_keep(self):
61 ## setup
62 mode = TrimmingMode.kpi
63 gappyness = 0.00
64 gaps = 0.9
65 parsimony_informative = True
66 constant_site = False
67
68 assert True == shouldKeep(
69 mode, parsimony_informative, constant_site, gappyness, gaps
70 )
71
72 def test_shouldKeep_kpi_trim(self):
73 ## setup
74 mode = TrimmingMode.kpi
75 gappyness = 0.95
76 gaps = 0.9
77 parsimony_informative = False
78 constant_site = False
79
80 assert False == shouldKeep(
81 mode, parsimony_informative, constant_site, gappyness, gaps
82 )
83
84 def test_shouldKeep_kpic_keep(self):
85 ## setup
86 mode = TrimmingMode.kpic
87 gappyness = 0.95
88 gaps = 0.9
89 parsimony_informative = False
90 constant_site = True
91
92 assert True == shouldKeep(
93 mode, parsimony_informative, constant_site, gappyness, gaps
94 )
95
96 def test_shouldKeep_kpic_trim(self):
97 ## setup
98 mode = TrimmingMode.kpic
99 gappyness = 0.95
100 gaps = 0.9
101 parsimony_informative = False
102 constant_site = False
103
104 assert False == shouldKeep(
105 mode, parsimony_informative, constant_site, gappyness, gaps
106 )
107
108 def test_shouldKeep_kpic_gappy_keep(self):
109 ## setup
110 mode = TrimmingMode.kpic_gappy
111 gappyness = 0.70
112 gaps = 0.9
113 parsimony_informative = False
114 constant_site = True
115
116 assert True == shouldKeep(
117 mode, parsimony_informative, constant_site, gappyness, gaps
118 )
119
120 def test_shouldKeep_kpic_gappy_trim(self):
121 ## setup
122 mode = TrimmingMode.kpic_gappy
123 gappyness = 0.95
124 gaps = 0.9
125 parsimony_informative = False
126 constant_site = True
127
128 assert False == shouldKeep(
129 mode, parsimony_informative, constant_site, gappyness, gaps
130 )
131
132 def test_gappy_mode(self):
133 ## setup
134 gappyness = 0.00
135 parsimony_informative = True
136 keepD = {}
137 trimD = {}
138 i = 2
139 gaps = 0.9
140 alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
141 use_log = False
142 constant_site = False
143
144 for entry in alignment:
145 keepD[entry.description] = np.empty([6], dtype=str)
146 trimD = {}
147 for entry in alignment:
148 trimD[entry.description] = np.empty([6], dtype=str)
149
150 ## execution
151 keepD, trimD = trim(
152 gappyness,
153 parsimony_informative,
154 constant_site,
155 keepD,
156 trimD,
157 i,
158 gaps,
159 alignment,
160 TrimmingMode.gappy,
161 use_log,
162 )
163
164 ## check results
165 expected_keepD = {
166 "1": np.array(["", "", "G", "", "", ""]),
167 "2": np.array(["", "", "G", "", "", ""]),
168 "3": np.array(["", "", "G", "", "", ""]),
169 "4": np.array(["", "", "A", "", "", ""]),
170 "5": np.array(["", "", "a", "", "", ""]),
171 }
172 expected_trimD = {
173 "1": np.array(["", "", "", "", "", ""]),
174 "2": np.array(["", "", "", "", "", ""]),
175 "3": np.array(["", "", "", "", "", ""]),
176 "4": np.array(["", "", "", "", "", ""]),
177 "5": np.array(["", "", "", "", "", ""]),
178 }
179
180 assert expected_keepD.keys() == keepD.keys()
181 assert all(
182 np.array_equal(expected_keepD[key], keepD[key]) for key in expected_keepD
183 )
184 assert expected_trimD.keys() == trimD.keys()
185 assert all(
186 np.array_equal(expected_trimD[key], trimD[key]) for key in expected_trimD
187 )
188
189 def test_kpi_gappy_mode(self):
190 ## setup
191 gappyness = 0.6
192 parsimony_informative = False
193 constant_site = True
194 keepD = {}
195 trimD = {}
196 i = 1
197 gaps = 0.9
198 alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
199 use_log = False
200
201 for entry in alignment:
202 keepD[entry.description] = np.empty([6], dtype=str)
203 trimD = {}
204 for entry in alignment:
205 trimD[entry.description] = np.empty([6], dtype=str)
206
207 ## execution
208 keepD, trimD = trim(
209 gappyness,
210 parsimony_informative,
211 constant_site,
212 keepD,
213 trimD,
214 i,
215 gaps,
216 alignment,
217 TrimmingMode.kpi_gappy,
218 use_log,
219 )
220
221 ## check results
222 expected_keepD = {
223 "1": np.array(["", "", "", "", "", ""]),
224 "2": np.array(["", "", "", "", "", ""]),
225 "3": np.array(["", "", "", "", "", ""]),
226 "4": np.array(["", "", "", "", "", ""]),
227 "5": np.array(["", "", "", "", "", ""]),
228 }
229 expected_trimD = {
230 "1": np.array(["", "-", "", "", "", ""]),
231 "2": np.array(["", "-", "", "", "", ""]),
232 "3": np.array(["", "-", "", "", "", ""]),
233 "4": np.array(["", "G", "", "", "", ""]),
234 "5": np.array(["", "C", "", "", "", ""]),
235 }
236
237 assert expected_keepD.keys() == keepD.keys()
238 assert all(
239 np.array_equal(expected_keepD[key], keepD[key]) for key in expected_keepD
240 )
241 assert expected_trimD.keys() == trimD.keys()
242 assert all(
243 np.array_equal(expected_trimD[key], trimD[key]) for key in expected_trimD
244 )
245
246 def test_kpi_mode(self):
247 ## setup
248 gappyness = 0.2
249 parsimony_informative = True
250 constant_site = False
251 keepD = {}
252 trimD = {}
253 i = 5
254 gaps = 0.9
255 alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
256 use_log = False
257
258 for entry in alignment:
259 keepD[entry.description] = np.empty([6], dtype=str)
260 trimD = {}
261 for entry in alignment:
262 trimD[entry.description] = np.empty([6], dtype=str)
263
264 ## execution
265 keepD, trimD = trim(
266 gappyness,
267 parsimony_informative,
268 constant_site,
269 keepD,
270 trimD,
271 i,
272 gaps,
273 alignment,
274 TrimmingMode.kpi,
275 use_log,
276 )
277
278 ## check results
279 expected_keepD = {
280 "1": np.array(["", "", "", "", "", "T"]),
281 "2": np.array(["", "", "", "", "", "T"]),
282 "3": np.array(["", "", "", "", "", "A"]),
283 "4": np.array(["", "", "", "", "", "A"]),
284 "5": np.array(["", "", "", "", "", "-"]),
285 }
286 expected_trimD = {
287 "1": np.array(["", "", "", "", "", ""]),
288 "2": np.array(["", "", "", "", "", ""]),
289 "3": np.array(["", "", "", "", "", ""]),
290 "4": np.array(["", "", "", "", "", ""]),
291 "5": np.array(["", "", "", "", "", ""]),
292 }
293
294 assert expected_keepD.keys() == keepD.keys()
295 assert all(
296 np.array_equal(expected_keepD[key], keepD[key]) for key in expected_keepD
297 )
298 assert expected_trimD.keys() == trimD.keys()
299 assert all(
300 np.array_equal(expected_trimD[key], trimD[key]) for key in expected_trimD
301 )
302
303 def test_kpic_mode(self):
304 ## setup
305 gappyness = 0.2
306 parsimony_informative = False
307 constant_site = True
308 keepD = {}
309 trimD = {}
310 i = 0
311 gaps = 0.9
312 alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
313 use_log = False
314
315 for entry in alignment:
316 keepD[entry.description] = np.empty([6], dtype=str)
317 trimD = {}
318 for entry in alignment:
319 trimD[entry.description] = np.empty([6], dtype=str)
320
321 ## execution
322 keepD, trimD = trim(
323 gappyness,
324 parsimony_informative,
325 constant_site,
326 keepD,
327 trimD,
328 i,
329 gaps,
330 alignment,
331 TrimmingMode.kpic,
332 use_log,
333 )
334
335 ## check results
336 expected_keepD = {
337 "1": np.array(["A", "", "", "", "", ""]),
338 "2": np.array(["A", "", "", "", "", ""]),
339 "3": np.array(["A", "", "", "", "", ""]),
340 "4": np.array(["A", "", "", "", "", ""]),
341 "5": np.array(["A", "", "", "", "", ""]),
342 }
343 expected_trimD = {
344 "1": np.array(["", "", "", "", "", ""]),
345 "2": np.array(["", "", "", "", "", ""]),
346 "3": np.array(["", "", "", "", "", ""]),
347 "4": np.array(["", "", "", "", "", ""]),
348 "5": np.array(["", "", "", "", "", ""]),
349 }
350
351 assert expected_keepD.keys() == keepD.keys()
352 assert all(
353 np.array_equal(expected_keepD[key], keepD[key]) for key in expected_keepD
354 )
355 assert expected_trimD.keys() == trimD.keys()
356 assert all(
357 np.array_equal(expected_trimD[key], trimD[key]) for key in expected_trimD
358 )
359
360 def test_kpic_gappy_mode(self):
361 ## setup
362 gappyness = 0.2
363 parsimony_informative = False
364 constant_site = False
365 keepD = {}
366 trimD = {}
367 i = 3
368 gaps = 0.9
369 alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
370 use_log = False
371
372 for entry in alignment:
373 keepD[entry.description] = np.empty([6], dtype=str)
374 trimD = {}
375 for entry in alignment:
376 trimD[entry.description] = np.empty([6], dtype=str)
377
378 ## execution
379 keepD, trimD = trim(
380 gappyness,
381 parsimony_informative,
382 constant_site,
383 keepD,
384 trimD,
385 i,
386 gaps,
387 alignment,
388 TrimmingMode.kpic_gappy,
389 use_log,
390 )
391
392 ## check results
393 expected_keepD = {
394 "1": np.array(["", "", "", "", "", ""]),
395 "2": np.array(["", "", "", "", "", ""]),
396 "3": np.array(["", "", "", "", "", ""]),
397 "4": np.array(["", "", "", "", "", ""]),
398 "5": np.array(["", "", "", "", "", ""]),
399 }
400 expected_trimD = {
401 "1": np.array(["", "", "", "T", "", ""]),
402 "2": np.array(["", "", "", "-", "", ""]),
403 "3": np.array(["", "", "", "-", "", ""]),
404 "4": np.array(["", "", "", "-", "", ""]),
405 "5": np.array(["", "", "", "-", "", ""]),
406 }
407
408 assert expected_keepD.keys() == keepD.keys()
409 assert all(
410 np.array_equal(expected_keepD[key], keepD[key]) for key in expected_keepD
411 )
412 assert expected_trimD.keys() == trimD.keys()
413 assert all(
414 np.array_equal(expected_trimD[key], trimD[key]) for key in expected_trimD
415 )