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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/statistics commit 7c5002672919ca1e5eacacb835a4ce66ffa19656
author bgruening
date Mon, 21 Nov 2022 18:07:45 +0000
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-1:000000000000 0:a3d8cadaf060
1 #!/usr/bin/env python
2
3 """
4
5 """
6 import argparse
7
8 import numpy as np
9 from scipy import stats
10
11
12 def columns_to_values(args, line):
13 # here you go over every list
14 samples = []
15 for i in args:
16 cols = line.split("\t")
17 sample_list = []
18 for row in i:
19 sample_list.append(cols[row - 1])
20 samples.append(list(map(int, sample_list)))
21 return samples
22
23
24 def main():
25 parser = argparse.ArgumentParser()
26 parser.add_argument("-i", "--infile", required=True, help="Tabular file.")
27 parser.add_argument(
28 "-o", "--outfile", required=True, help="Path to the output file."
29 )
30 parser.add_argument("--sample_one_cols", help="Input format, like smi, sdf, inchi")
31 parser.add_argument("--sample_two_cols", help="Input format, like smi, sdf, inchi")
32 parser.add_argument(
33 "--sample_cols",
34 help="Input format, like smi, sdf, inchi,separate arrays using ;",
35 )
36 parser.add_argument("--test_id", help="statistical test method")
37 parser.add_argument(
38 "--mwu_use_continuity",
39 action="store_true",
40 default=False,
41 help="Whether a continuity correction (1/2.) should be taken into account.",
42 )
43 parser.add_argument(
44 "--equal_var",
45 action="store_true",
46 default=False,
47 help="If set perform a standard independent 2 sample test that assumes equal population variances. If not set, perform Welch's t-test, which does not assume equal population variance.",
48 )
49 parser.add_argument(
50 "--reta",
51 action="store_true",
52 default=False,
53 help="Whether or not to return the internally computed a values.",
54 )
55 parser.add_argument(
56 "--fisher",
57 action="store_true",
58 default=False,
59 help="if true then Fisher definition is used",
60 )
61 parser.add_argument(
62 "--bias",
63 action="store_true",
64 default=False,
65 help="if false,then the calculations are corrected for statistical bias",
66 )
67 parser.add_argument(
68 "--inclusive1",
69 action="store_true",
70 default=False,
71 help="if false,lower_limit will be ignored",
72 )
73 parser.add_argument(
74 "--inclusive2",
75 action="store_true",
76 default=False,
77 help="if false,higher_limit will be ignored",
78 )
79 parser.add_argument(
80 "--inclusive",
81 action="store_true",
82 default=False,
83 help="if false,limit will be ignored",
84 )
85 parser.add_argument(
86 "--printextras",
87 action="store_true",
88 default=False,
89 help="If True, if there are extra points a warning is raised saying how many of those points there are",
90 )
91 parser.add_argument(
92 "--initial_lexsort",
93 action="store_true",
94 default="False",
95 help="Whether to use lexsort or quicksort as the sorting method for the initial sort of the inputs.",
96 )
97 parser.add_argument(
98 "--correction",
99 action="store_true",
100 default=False,
101 help="continuity correction ",
102 )
103 parser.add_argument(
104 "--axis",
105 type=int,
106 default=0,
107 help="Axis can equal None (ravel array first), or an integer (the axis over which to operate on a and b)",
108 )
109 parser.add_argument(
110 "--n",
111 type=int,
112 default=0,
113 help="the number of trials. This is ignored if x gives both the number of successes and failures",
114 )
115 parser.add_argument(
116 "--b", type=int, default=0, help="The number of bins to use for the histogram"
117 )
118 parser.add_argument(
119 "--N", type=int, default=0, help="Score that is compared to the elements in a."
120 )
121 parser.add_argument(
122 "--ddof", type=int, default=0, help="Degrees of freedom correction"
123 )
124 parser.add_argument(
125 "--score",
126 type=int,
127 default=0,
128 help="Score that is compared to the elements in a.",
129 )
130 parser.add_argument("--m", type=float, default=0.0, help="limits")
131 parser.add_argument("--mf", type=float, default=2.0, help="lower limit")
132 parser.add_argument("--nf", type=float, default=99.9, help="higher_limit")
133 parser.add_argument(
134 "--p",
135 type=float,
136 default=0.5,
137 help="The hypothesized probability of success. 0 <= p <= 1. The default value is p = 0.5",
138 )
139 parser.add_argument("--alpha", type=float, default=0.9, help="probability")
140 parser.add_argument(
141 "--new",
142 type=float,
143 default=0.0,
144 help="Value to put in place of values in a outside of bounds",
145 )
146 parser.add_argument(
147 "--proportiontocut",
148 type=float,
149 default=0.0,
150 help="Proportion (in range 0-1) of total data set to trim of each end.",
151 )
152 parser.add_argument(
153 "--lambda_",
154 type=float,
155 default=1.0,
156 help="lambda_ gives the power in the Cressie-Read power divergence statistic",
157 )
158 parser.add_argument(
159 "--imbda",
160 type=float,
161 default=0,
162 help="If lmbda is not None, do the transformation for that value.If lmbda is None, find the lambda that maximizes the log-likelihood function and return it as the second output argument.",
163 )
164 parser.add_argument(
165 "--base",
166 type=float,
167 default=1.6,
168 help="The logarithmic base to use, defaults to e",
169 )
170 parser.add_argument("--dtype", help="dtype")
171 parser.add_argument("--med", help="med")
172 parser.add_argument("--cdf", help="cdf")
173 parser.add_argument("--zero_method", help="zero_method options")
174 parser.add_argument("--dist", help="dist options")
175 parser.add_argument("--ties", help="ties options")
176 parser.add_argument("--alternative", help="alternative options")
177 parser.add_argument("--mode", help="mode options")
178 parser.add_argument("--method", help="method options")
179 parser.add_argument("--md", help="md options")
180 parser.add_argument("--center", help="center options")
181 parser.add_argument("--kind", help="kind options")
182 parser.add_argument("--tail", help="tail options")
183 parser.add_argument("--interpolation", help="interpolation options")
184 parser.add_argument("--statistic", help="statistic options")
185
186 args = parser.parse_args()
187 infile = args.infile
188 outfile = open(args.outfile, "w+")
189 test_id = args.test_id
190 nf = args.nf
191 mf = args.mf
192 imbda = args.imbda
193 inclusive1 = args.inclusive1
194 inclusive2 = args.inclusive2
195 sample0 = 0
196 sample1 = 0
197 sample2 = 0
198 if args.sample_cols is not None:
199 sample0 = 1
200 barlett_samples = []
201 for sample in args.sample_cols.split(";"):
202 barlett_samples.append(list(map(int, sample.split(","))))
203 if args.sample_one_cols is not None:
204 sample1 = 1
205 sample_one_cols = args.sample_one_cols.split(",")
206 if args.sample_two_cols is not None:
207 sample_two_cols = args.sample_two_cols.split(",")
208 sample2 = 1
209 for line in open(infile):
210 sample_one = []
211 sample_two = []
212 cols = line.strip().split("\t")
213 if sample0 == 1:
214 b_samples = columns_to_values(barlett_samples, line)
215 if sample1 == 1:
216 for index in sample_one_cols:
217 sample_one.append(cols[int(index) - 1])
218 if sample2 == 1:
219 for index in sample_two_cols:
220 sample_two.append(cols[int(index) - 1])
221 if test_id.strip() == "describe":
222 size, min_max, mean, uv, bs, bk = stats.describe(
223 list(map(float, sample_one))
224 )
225 cols.append(size)
226 cols.append(min_max)
227 cols.append(mean)
228 cols.append(uv)
229 cols.append(bs)
230 cols.append(bk)
231 elif test_id.strip() == "mode":
232 vals, counts = stats.mode(list(map(float, sample_one)))
233 cols.append(vals)
234 cols.append(counts)
235 elif test_id.strip() == "nanmean":
236 m = stats.nanmean(list(map(float, sample_one)))
237 cols.append(m)
238 elif test_id.strip() == "nanmedian":
239 m = stats.nanmedian(list(map(float, sample_one)))
240 cols.append(m)
241 elif test_id.strip() == "kurtosistest":
242 z_value, p_value = stats.kurtosistest(list(map(float, sample_one)))
243 cols.append(z_value)
244 cols.append(p_value)
245 elif test_id.strip() == "variation":
246 ra = stats.variation(list(map(float, sample_one)))
247 cols.append(ra)
248 elif test_id.strip() == "itemfreq":
249 freq = np.unique(list(map(float, sample_one)), return_counts=True)
250 for i in freq:
251 elements = ",".join(list(map(str, i)))
252 cols.append(elements)
253 elif test_id.strip() == "nanmedian":
254 m = stats.nanmedian(list(map(float, sample_one)))
255 cols.append(m)
256 elif test_id.strip() == "variation":
257 ra = stats.variation(list(map(float, sample_one)))
258 cols.append(ra)
259 elif test_id.strip() == "boxcox_llf":
260 IIf = stats.boxcox_llf(imbda, list(map(float, sample_one)))
261 cols.append(IIf)
262 elif test_id.strip() == "tiecorrect":
263 fa = stats.tiecorrect(list(map(float, sample_one)))
264 cols.append(fa)
265 elif test_id.strip() == "rankdata":
266 r = stats.rankdata(list(map(float, sample_one)), method=args.md)
267 cols.append(r)
268 elif test_id.strip() == "nanstd":
269 s = stats.nanstd(list(map(float, sample_one)), bias=args.bias)
270 cols.append(s)
271 elif test_id.strip() == "anderson":
272 A2, critical, sig = stats.anderson(
273 list(map(float, sample_one)), dist=args.dist
274 )
275 cols.append(A2)
276 for i in critical:
277 cols.append(i)
278 cols.append(",")
279 for i in sig:
280 cols.append(i)
281 elif test_id.strip() == "binom_test":
282 p_value = stats.binom_test(list(map(float, sample_one)), n=args.n, p=args.p)
283 cols.append(p_value)
284 elif test_id.strip() == "gmean":
285 gm = stats.gmean(list(map(float, sample_one)), dtype=args.dtype)
286 cols.append(gm)
287 elif test_id.strip() == "hmean":
288 hm = stats.hmean(list(map(float, sample_one)), dtype=args.dtype)
289 cols.append(hm)
290 elif test_id.strip() == "kurtosis":
291 k = stats.kurtosis(
292 list(map(float, sample_one)),
293 axis=args.axis,
294 fisher=args.fisher,
295 bias=args.bias,
296 )
297 cols.append(k)
298 elif test_id.strip() == "moment":
299 n_moment = stats.moment(list(map(float, sample_one)), n=args.n)
300 cols.append(n_moment)
301 elif test_id.strip() == "normaltest":
302 k2, p_value = stats.normaltest(list(map(float, sample_one)))
303 cols.append(k2)
304 cols.append(p_value)
305 elif test_id.strip() == "skew":
306 skewness = stats.skew(list(map(float, sample_one)), bias=args.bias)
307 cols.append(skewness)
308 elif test_id.strip() == "skewtest":
309 z_value, p_value = stats.skewtest(list(map(float, sample_one)))
310 cols.append(z_value)
311 cols.append(p_value)
312 elif test_id.strip() == "sem":
313 s = stats.sem(list(map(float, sample_one)), ddof=args.ddof)
314 cols.append(s)
315 elif test_id.strip() == "zscore":
316 z = stats.zscore(list(map(float, sample_one)), ddof=args.ddof)
317 for i in z:
318 cols.append(i)
319 elif test_id.strip() == "signaltonoise":
320 s2n = stats.signaltonoise(list(map(float, sample_one)), ddof=args.ddof)
321 cols.append(s2n)
322 elif test_id.strip() == "percentileofscore":
323 p = stats.percentileofscore(
324 list(map(float, sample_one)), score=args.score, kind=args.kind
325 )
326 cols.append(p)
327 elif test_id.strip() == "bayes_mvs":
328 c_mean, c_var, c_std = stats.bayes_mvs(
329 list(map(float, sample_one)), alpha=args.alpha
330 )
331 cols.append(c_mean)
332 cols.append(c_var)
333 cols.append(c_std)
334 elif test_id.strip() == "sigmaclip":
335 c, c_low, c_up = stats.sigmaclip(
336 list(map(float, sample_one)), low=args.m, high=args.n
337 )
338 cols.append(c)
339 cols.append(c_low)
340 cols.append(c_up)
341 elif test_id.strip() == "kstest":
342 d, p_value = stats.kstest(
343 list(map(float, sample_one)),
344 cdf=args.cdf,
345 N=args.N,
346 alternative=args.alternative,
347 mode=args.mode,
348 )
349 cols.append(d)
350 cols.append(p_value)
351 elif test_id.strip() == "chi2_contingency":
352 chi2, p, dof, ex = stats.chi2_contingency(
353 list(map(float, sample_one)),
354 correction=args.correction,
355 lambda_=args.lambda_,
356 )
357 cols.append(chi2)
358 cols.append(p)
359 cols.append(dof)
360 cols.append(ex)
361 elif test_id.strip() == "tmean":
362 if nf == 0 and mf == 0:
363 mean = stats.tmean(list(map(float, sample_one)))
364 else:
365 mean = stats.tmean(
366 list(map(float, sample_one)), (mf, nf), (inclusive1, inclusive2)
367 )
368 cols.append(mean)
369 elif test_id.strip() == "tmin":
370 if mf == 0:
371 min = stats.tmin(list(map(float, sample_one)))
372 else:
373 min = stats.tmin(
374 list(map(float, sample_one)),
375 lowerlimit=mf,
376 inclusive=args.inclusive,
377 )
378 cols.append(min)
379 elif test_id.strip() == "tmax":
380 if nf == 0:
381 max = stats.tmax(list(map(float, sample_one)))
382 else:
383 max = stats.tmax(
384 list(map(float, sample_one)),
385 upperlimit=nf,
386 inclusive=args.inclusive,
387 )
388 cols.append(max)
389 elif test_id.strip() == "tvar":
390 if nf == 0 and mf == 0:
391 var = stats.tvar(list(map(float, sample_one)))
392 else:
393 var = stats.tvar(
394 list(map(float, sample_one)), (mf, nf), (inclusive1, inclusive2)
395 )
396 cols.append(var)
397 elif test_id.strip() == "tstd":
398 if nf == 0 and mf == 0:
399 std = stats.tstd(list(map(float, sample_one)))
400 else:
401 std = stats.tstd(
402 list(map(float, sample_one)), (mf, nf), (inclusive1, inclusive2)
403 )
404 cols.append(std)
405 elif test_id.strip() == "tsem":
406 if nf == 0 and mf == 0:
407 s = stats.tsem(list(map(float, sample_one)))
408 else:
409 s = stats.tsem(
410 list(map(float, sample_one)), (mf, nf), (inclusive1, inclusive2)
411 )
412 cols.append(s)
413 elif test_id.strip() == "scoreatpercentile":
414 if nf == 0 and mf == 0:
415 s = stats.scoreatpercentile(
416 list(map(float, sample_one)),
417 list(map(float, sample_two)),
418 interpolation_method=args.interpolation,
419 )
420 else:
421 s = stats.scoreatpercentile(
422 list(map(float, sample_one)),
423 list(map(float, sample_two)),
424 (mf, nf),
425 interpolation_method=args.interpolation,
426 )
427 for i in s:
428 cols.append(i)
429 elif test_id.strip() == "relfreq":
430 if nf == 0 and mf == 0:
431 rel, low_range, binsize, ex = stats.relfreq(
432 list(map(float, sample_one)), args.b
433 )
434 else:
435 rel, low_range, binsize, ex = stats.relfreq(
436 list(map(float, sample_one)), args.b, (mf, nf)
437 )
438 for i in rel:
439 cols.append(i)
440 cols.append(low_range)
441 cols.append(binsize)
442 cols.append(ex)
443 elif test_id.strip() == "binned_statistic":
444 if nf == 0 and mf == 0:
445 st, b_edge, b_n = stats.binned_statistic(
446 list(map(float, sample_one)),
447 list(map(float, sample_two)),
448 statistic=args.statistic,
449 bins=args.b,
450 )
451 else:
452 st, b_edge, b_n = stats.binned_statistic(
453 list(map(float, sample_one)),
454 list(map(float, sample_two)),
455 statistic=args.statistic,
456 bins=args.b,
457 range=(mf, nf),
458 )
459 cols.append(st)
460 cols.append(b_edge)
461 cols.append(b_n)
462 elif test_id.strip() == "threshold":
463 if nf == 0 and mf == 0:
464 o = stats.threshold(list(map(float, sample_one)), newval=args.new)
465 else:
466 o = stats.threshold(
467 list(map(float, sample_one)), mf, nf, newval=args.new
468 )
469 for i in o:
470 cols.append(i)
471 elif test_id.strip() == "trimboth":
472 o = stats.trimboth(
473 list(map(float, sample_one)), proportiontocut=args.proportiontocut
474 )
475 for i in o:
476 cols.append(i)
477 elif test_id.strip() == "trim1":
478 t1 = stats.trim1(
479 list(map(float, sample_one)),
480 proportiontocut=args.proportiontocut,
481 tail=args.tail,
482 )
483 for i in t1:
484 cols.append(i)
485 elif test_id.strip() == "histogram":
486 if nf == 0 and mf == 0:
487 hi, low_range, binsize, ex = stats.histogram(
488 list(map(float, sample_one)), args.b
489 )
490 else:
491 hi, low_range, binsize, ex = stats.histogram(
492 list(map(float, sample_one)), args.b, (mf, nf)
493 )
494 cols.append(hi)
495 cols.append(low_range)
496 cols.append(binsize)
497 cols.append(ex)
498 elif test_id.strip() == "cumfreq":
499 if nf == 0 and mf == 0:
500 cum, low_range, binsize, ex = stats.cumfreq(
501 list(map(float, sample_one)), args.b
502 )
503 else:
504 cum, low_range, binsize, ex = stats.cumfreq(
505 list(map(float, sample_one)), args.b, (mf, nf)
506 )
507 cols.append(cum)
508 cols.append(low_range)
509 cols.append(binsize)
510 cols.append(ex)
511 elif test_id.strip() == "boxcox_normmax":
512 if nf == 0 and mf == 0:
513 ma = stats.boxcox_normmax(list(map(float, sample_one)))
514 else:
515 ma = stats.boxcox_normmax(
516 list(map(float, sample_one)), (mf, nf), method=args.method
517 )
518 cols.append(ma)
519 elif test_id.strip() == "boxcox":
520 if imbda == 0:
521 box, ma, ci = stats.boxcox(
522 list(map(float, sample_one)), alpha=args.alpha
523 )
524 cols.append(box)
525 cols.append(ma)
526 cols.append(ci)
527 else:
528 box = stats.boxcox(
529 list(map(float, sample_one)), imbda, alpha=args.alpha
530 )
531 cols.append(box)
532 elif test_id.strip() == "histogram2":
533 h2 = stats.histogram2(
534 list(map(float, sample_one)), list(map(float, sample_two))
535 )
536 for i in h2:
537 cols.append(i)
538 elif test_id.strip() == "ranksums":
539 z_statistic, p_value = stats.ranksums(
540 list(map(float, sample_one)), list(map(float, sample_two))
541 )
542 cols.append(z_statistic)
543 cols.append(p_value)
544 elif test_id.strip() == "ttest_1samp":
545 t, prob = stats.ttest_1samp(map(float, sample_one), map(float, sample_two))
546 for i in t:
547 cols.append(i)
548 for i in prob:
549 cols.append(i)
550 elif test_id.strip() == "ansari":
551 AB, p_value = stats.ansari(
552 list(map(float, sample_one)), list(map(float, sample_two))
553 )
554 cols.append(AB)
555 cols.append(p_value)
556 elif test_id.strip() == "linregress":
557 slope, intercept, r_value, p_value, stderr = stats.linregress(
558 list(map(float, sample_one)), list(map(float, sample_two))
559 )
560 cols.append(slope)
561 cols.append(intercept)
562 cols.append(r_value)
563 cols.append(p_value)
564 cols.append(stderr)
565 elif test_id.strip() == "pearsonr":
566 cor, p_value = stats.pearsonr(
567 list(map(float, sample_one)), list(map(float, sample_two))
568 )
569 cols.append(cor)
570 cols.append(p_value)
571 elif test_id.strip() == "pointbiserialr":
572 r, p_value = stats.pointbiserialr(
573 list(map(float, sample_one)), list(map(float, sample_two))
574 )
575 cols.append(r)
576 cols.append(p_value)
577 elif test_id.strip() == "ks_2samp":
578 d, p_value = stats.ks_2samp(
579 list(map(float, sample_one)), list(map(float, sample_two))
580 )
581 cols.append(d)
582 cols.append(p_value)
583 elif test_id.strip() == "mannwhitneyu":
584 mw_stats_u, p_value = stats.mannwhitneyu(
585 list(map(float, sample_one)),
586 list(map(float, sample_two)),
587 use_continuity=args.mwu_use_continuity,
588 )
589 cols.append(mw_stats_u)
590 cols.append(p_value)
591 elif test_id.strip() == "zmap":
592 z = stats.zmap(
593 list(map(float, sample_one)),
594 list(map(float, sample_two)),
595 ddof=args.ddof,
596 )
597 for i in z:
598 cols.append(i)
599 elif test_id.strip() == "ttest_ind":
600 mw_stats_u, p_value = stats.ttest_ind(
601 list(map(float, sample_one)),
602 list(map(float, sample_two)),
603 equal_var=args.equal_var,
604 )
605 cols.append(mw_stats_u)
606 cols.append(p_value)
607 elif test_id.strip() == "ttest_rel":
608 t, prob = stats.ttest_rel(
609 list(map(float, sample_one)),
610 list(map(float, sample_two)),
611 axis=args.axis,
612 )
613 cols.append(t)
614 cols.append(prob)
615 elif test_id.strip() == "mood":
616 z, p_value = stats.mood(
617 list(map(float, sample_one)),
618 list(map(float, sample_two)),
619 axis=args.axis,
620 )
621 cols.append(z)
622 cols.append(p_value)
623 elif test_id.strip() == "shapiro":
624 W, p_value = stats.shapiro(list(map(float, sample_one)))
625 cols.append(W)
626 cols.append(p_value)
627 elif test_id.strip() == "kendalltau":
628 k, p_value = stats.kendalltau(
629 list(map(float, sample_one)),
630 list(map(float, sample_two)),
631 initial_lexsort=args.initial_lexsort,
632 )
633 cols.append(k)
634 cols.append(p_value)
635 elif test_id.strip() == "entropy":
636 s = stats.entropy(
637 list(map(float, sample_one)),
638 list(map(float, sample_two)),
639 base=args.base,
640 )
641 cols.append(s)
642 elif test_id.strip() == "spearmanr":
643 if sample2 == 1:
644 rho, p_value = stats.spearmanr(
645 list(map(float, sample_one)), list(map(float, sample_two))
646 )
647 else:
648 rho, p_value = stats.spearmanr(list(map(float, sample_one)))
649 cols.append(rho)
650 cols.append(p_value)
651 elif test_id.strip() == "wilcoxon":
652 if sample2 == 1:
653 T, p_value = stats.wilcoxon(
654 list(map(float, sample_one)),
655 list(map(float, sample_two)),
656 zero_method=args.zero_method,
657 correction=args.correction,
658 )
659 else:
660 T, p_value = stats.wilcoxon(
661 list(map(float, sample_one)),
662 zero_method=args.zero_method,
663 correction=args.correction,
664 )
665 cols.append(T)
666 cols.append(p_value)
667 elif test_id.strip() == "chisquare":
668 if sample2 == 1:
669 rho, p_value = stats.chisquare(
670 list(map(float, sample_one)),
671 list(map(float, sample_two)),
672 ddof=args.ddof,
673 )
674 else:
675 rho, p_value = stats.chisquare(
676 list(map(float, sample_one)), ddof=args.ddof
677 )
678 cols.append(rho)
679 cols.append(p_value)
680 elif test_id.strip() == "power_divergence":
681 if sample2 == 1:
682 stat, p_value = stats.power_divergence(
683 list(map(float, sample_one)),
684 list(map(float, sample_two)),
685 ddof=args.ddof,
686 lambda_=args.lambda_,
687 )
688 else:
689 stat, p_value = stats.power_divergence(
690 list(map(float, sample_one)), ddof=args.ddof, lambda_=args.lambda_
691 )
692 cols.append(stat)
693 cols.append(p_value)
694 elif test_id.strip() == "theilslopes":
695 if sample2 == 1:
696 mpe, met, lo, up = stats.theilslopes(
697 list(map(float, sample_one)),
698 list(map(float, sample_two)),
699 alpha=args.alpha,
700 )
701 else:
702 mpe, met, lo, up = stats.theilslopes(
703 list(map(float, sample_one)), alpha=args.alpha
704 )
705 cols.append(mpe)
706 cols.append(met)
707 cols.append(lo)
708 cols.append(up)
709 elif test_id.strip() == "combine_pvalues":
710 if sample2 == 1:
711 stat, p_value = stats.combine_pvalues(
712 list(map(float, sample_one)),
713 method=args.med,
714 weights=list(map(float, sample_two)),
715 )
716 else:
717 stat, p_value = stats.combine_pvalues(
718 list(map(float, sample_one)), method=args.med
719 )
720 cols.append(stat)
721 cols.append(p_value)
722 elif test_id.strip() == "obrientransform":
723 ob = stats.obrientransform(*b_samples)
724 for i in ob:
725 elements = ",".join(list(map(str, i)))
726 cols.append(elements)
727 elif test_id.strip() == "f_oneway":
728 f_value, p_value = stats.f_oneway(*b_samples)
729 cols.append(f_value)
730 cols.append(p_value)
731 elif test_id.strip() == "kruskal":
732 h, p_value = stats.kruskal(*b_samples)
733 cols.append(h)
734 cols.append(p_value)
735 elif test_id.strip() == "friedmanchisquare":
736 fr, p_value = stats.friedmanchisquare(*b_samples)
737 cols.append(fr)
738 cols.append(p_value)
739 elif test_id.strip() == "fligner":
740 xsq, p_value = stats.fligner(
741 center=args.center, proportiontocut=args.proportiontocut, *b_samples
742 )
743 cols.append(xsq)
744 cols.append(p_value)
745 elif test_id.strip() == "bartlett":
746 T, p_value = stats.bartlett(*b_samples)
747 cols.append(T)
748 cols.append(p_value)
749 elif test_id.strip() == "levene":
750 w, p_value = stats.levene(
751 center=args.center, proportiontocut=args.proportiontocut, *b_samples
752 )
753 cols.append(w)
754 cols.append(p_value)
755 elif test_id.strip() == "median_test":
756 stat, p_value, m, table = stats.median_test(
757 ties=args.ties,
758 correction=args.correction,
759 lambda_=args.lambda_,
760 *b_samples
761 )
762 cols.append(stat)
763 cols.append(p_value)
764 cols.append(m)
765 cols.append(table)
766 for i in table:
767 elements = ",".join(list(map(str, i)))
768 cols.append(elements)
769 outfile.write("%s\n" % "\t".join(list(map(str, cols))))
770 outfile.close()
771
772
773 if __name__ == "__main__":
774 main()