Mercurial > repos > iuc > hyphy_busted

comparison test-data/bgm-out1.json @ 1:b678fe748dc5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:22:30 -0400
parents
children f8d88dcef64e
comparison
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0:edabb77ac0d4 1:b678fe748dc5
1 {
2 "MLE":{
3 "content": [
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243 [20, 30, 0.003095558108305428, 0.02500421480139507, 0.0280997729097005, 3, 2, 0],
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246 [21, 24, 0.0291189462349777, 0.004949542712431419, 0.03406848894740912, 5, 2, 0],
247 [21, 25, 0.05817486040851345, 0.2337789498314103, 0.2919538102399237, 5, 3, 3],
248 [21, 26, 0.02161672916870432, 0.01542046740137113, 0.03703719657007545, 5, 1, 1],
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250 [21, 29, 0.01104149126852355, 0.0112121954071869, 0.02225368667571045, 5, 2, 1],
251 [21, 30, 0.01981188214469076, 0.04607061916870642, 0.06588250131339718, 5, 2, 2],
252 [22, 23, 0.2417023075963993, 0.09748281763954433, 0.3391851252359436, 5, 3, 3],
253 [22, 24, 0.02866820036560731, 0.004389002955129634, 0.03305720332073694, 5, 2, 1],
254 [22, 25, 0.05951378230290671, 0.2182001187994253, 0.277713901102332, 5, 3, 3],
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258 [22, 30, 0.01671073245892866, 0.04349804879476411, 0.06020878125369277, 5, 2, 2],
259 [23, 24, 0.04562441011343223, 0.02002989348257047, 0.0656543035960027, 3, 2, 1],
260 [23, 25, 0.002681149687355626, 0.02379196502622149, 0.02647311471357712, 3, 3, 1],
261 [23, 26, 0.02520734946693424, 0.08017222321450257, 0.1053795726814368, 3, 1, 1],
262 [23, 28, 0.006108324165705776, 0.01315945866988892, 0.0192677828355947, 3, 2, 0],
263 [23, 29, 0.007832385982193907, 0.01244156292841715, 0.02027394891061106, 3, 2, 0],
264 [23, 30, 0.002148132526385406, 0.0162182445937851, 0.0183663771201705, 3, 2, 0],
265 [24, 25, 0.003280169877064053, 0.04232444793320719, 0.04560461781027124, 2, 3, 0],
266 [24, 26, 0.005616845573718578, 0.03457432648711956, 0.04019117206083814, 2, 1, 0],
267 [24, 28, 0.01662564599904145, 0.08682615622766726, 0.1034518022267087, 2, 2, 1],
268 [24, 29, 0.02380609019454122, 0.08066548140193953, 0.1044715715964808, 2, 2, 1],
269 [24, 30, 0.001779848103066491, 0.03558210318886525, 0.03736195129193174, 2, 2, 0],
270 [25, 26, 0.06593316758122636, 0.02166592663716863, 0.08759909421839499, 3, 1, 1],
271 [25, 28, 0.02889704020936961, 0.005342768040509653, 0.03423980824987927, 3, 2, 1],
272 [25, 29, 0.02814406496232846, 0.01687874749838335, 0.04502281246071182, 3, 2, 1],
273 [25, 30, 0.1123773177282409, 0.107330048901509, 0.2197073666297499, 3, 2, 2],
274 [26, 28, 0.01202310187965289, 0.0100752849569055, 0.0220983868365584, 1, 2, 0],
275 [26, 29, 0.01098659894875614, 0.0106778458846393, 0.02166444483339544, 1, 2, 0],
276 [26, 30, 0.008888531742284057, 0.0220072024775357, 0.03089573421981976, 1, 2, 0],
277 [28, 29, 0.3253931306175987, 0.3786081317863912, 0.70400126240399, 2, 2, 2],
278 [28, 30, 0.007946759742122602, 0.03360599467213372, 0.04155275441425633, 2, 2, 1],
279 [29, 30, 0.01669873349292508, 0.03504162520377113, 0.05174035869669621, 2, 2, 1]
280 ],
281 "headers": [
282 ["Site 1", "Index of site 1"],
283 ["Site 2", "Index of site 2"],
284 ["P [Site 1 –> Site 2]", "Probability that site 2 is conditionally dependent on site 1"],
285 ["P [Site 2 –> Site 1]", "Probability that site 1 is conditionally dependent on site 2"],
286 ["P [Site 1 <–> Site 2]", "Probability that sites 1 and 2 are not conditionally independent"],
287 ["Site 1 subs", "Substitution counts inferred for Site 1"],
288 ["Site 2 subs", "Substitution counts inferred for Site 2"],
289 ["Shared subs", "Substitutions shared by both sites"]
290 ]
291 },
292 "analysis":{
293 "authors":"Art FY Poon, Fraser I Lewis, Simon DW Frost and Sergei L Kosakovsky Pond",
294 "citation":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950",
295 "contact":"apoon42@uwo.ca",
296 "info":"BGM (Bayesian Graphical Model) uses a maximum likelihood ancestral state reconstruction to\nmap substitution (non-synonymous only for coding data) events to branches in the\nphylogeny and then analyzes the joint distribution of the\nsubstitution map using a Bayesian graphical model (network).\nNext, a Markov chain Monte Carlo analysis is used to generate\na random sample of network structures from the posterior\ndistribution given the data. Each node in the network\nrepresents a codon site in the alignment, and links (edges)\nbetween nodes indicate high posterior support for correlated\nsubstitutions at the two sites over time, which implies coevolution.",
297 "requirements":"in-frame codon alignment and a phylogenetic tree",
298 "version":"1.1"
299 },
300 "branch attributes":{
301 "0":{
302 "Baboon":{
303 "models.DNA.GTR.ModelDescription":0
304 },
305 "Cat":{
306 "models.DNA.GTR.ModelDescription":0.7933191636859576
307 },
308 "Chimp":{
309 "models.DNA.GTR.ModelDescription":0
310 },
311 "Cow":{
312 "models.DNA.GTR.ModelDescription":0.8094119333244753
313 },
314 "Horse":{
315 "models.DNA.GTR.ModelDescription":0.2769077630163064
316 },
317 "Human":{
318 "models.DNA.GTR.ModelDescription":0
319 },
320 "Mouse":{
321 "models.DNA.GTR.ModelDescription":0.1094921058577506
322 },
323 "Node1":{
324 "models.DNA.GTR.ModelDescription":0.4820782253393885
325 },
326 "Node12":{
327 "models.DNA.GTR.ModelDescription":0
328 },
329 "Node2":{
330 "models.DNA.GTR.ModelDescription":0.08259105925424247
331 },
332 "Node3":{
333 "models.DNA.GTR.ModelDescription":0.2526911684326281
334 },
335 "Node8":{
336 "models.DNA.GTR.ModelDescription":0.06531857233184223
337 },
338 "Node9":{
339 "models.DNA.GTR.ModelDescription":0.03361817454867485
340 },
341 "Pig":{
342 "models.DNA.GTR.ModelDescription":0
343 },
344 "Rat":{
345 "models.DNA.GTR.ModelDescription":0.0888784436278628
346 },
347 "RhMonkey":{
348 "models.DNA.GTR.ModelDescription":0
349 }
350 },
351 "attributes":{
352 "models.DNA.GTR.ModelDescription":{
353 "attribute type":"branch length",
354 "display order":0
355 }
356 }
357 },
358 "data partitions":{
359 "0":{
360 "coverage": [
361 [0, 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]
362 ],
363 "name":"bgm.filter.default"
364 }
365 },
366 "fits":{
367 "models.DNA.GTR.ModelDescription":{
368 "AIC-c":472.7691802214979,
369 "Log Likelihood":-210.2027719289308,
370 "Rate Distributions":null,
371 "display order":0,
372 "estimated parameters":24
373 }
374 },
375 "input":{
376 "datatype":"nucleotide",
377 "file name":"/tmp/tmpSz4m4X/job_working_directory/000/3/working/bgm_input.fa",
378 "number of sequences":10,
379 "number of sites":30,
380 "trees":{
381 "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"
382 }
383 },
384 "settings":{
385 "burn-in":10000,
386 "data-type":"nucleotide",
387 "max-parents":1,
388 "min-subs":1,
389 "samples":100,
390 "steps":100000,
391 "threshold":0.5
392 },
393 "tested":0,
394 "timers":{
395 "Baseline fit":{
396 "order":1,
397 "timer":0
398 },
399 "Network inference":{
400 "order":2,
401 "timer":1
402 },
403 "Overall":{
404 "order":0,
405 "timer":1
406 }
407 }
408 }