Mercurial > repos > iuc > hyphy_slac
diff test-data/bgm-out1.json @ 1:c2bed8cc8fc1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
| author | iuc |
|---|---|
| date | Wed, 21 Aug 2019 12:27:21 -0400 |
| parents | |
| children | a603e2f909e5 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-out1.json Wed Aug 21 12:27:21 2019 -0400 @@ -0,0 +1,408 @@ +{ + "MLE":{ + "content": [ +[3, 4, 0.01806536842133838, 0.0196151052739404, 0.03768047369527878, 2, 4, 1], + [3, 5, 0.0136689326165866, 0.08411879896894461, 0.09778773158553121, 2, 2, 1], + [3, 6, 0.01626880980001384, 0.05621779910581199, 0.07248660890582583, 2, 2, 1], + [3, 7, 0.01296085994820069, 0.02206081801264715, 0.03502167796084783, 2, 1, 0], + [3, 9, 0.01069476203525126, 0.01376808584576788, 0.02446284788101914, 2, 3, 0], + [3, 10, 0.05465425513197631, 0.1433115560788012, 0.1979658112107776, 2, 1, 1], + [3, 11, 0.02893963856420952, 0.01605584764833427, 0.04499548621254379, 2, 1, 0], + [3, 12, 0.01072516405613842, 0.0249434485528662, 0.03566861260900463, 2, 1, 0], + [3, 14, 0.02105948857071199, 0.05408645518169206, 0.07514594375240405, 2, 2, 1], + [3, 15, 0.0123000231875007, 0.02432900062064017, 0.03662902380814088, 2, 3, 1], + [3, 16, 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0], + [28, 29, 0.3253931306175987, 0.3786081317863912, 0.70400126240399, 2, 2, 2], + [28, 30, 0.007946759742122602, 0.03360599467213372, 0.04155275441425633, 2, 2, 1], + [29, 30, 0.01669873349292508, 0.03504162520377113, 0.05174035869669621, 2, 2, 1] + ], + "headers": [ +["Site 1", "Index of site 1"], + ["Site 2", "Index of site 2"], + ["P [Site 1 –> Site 2]", "Probability that site 2 is conditionally dependent on site 1"], + ["P [Site 2 –> Site 1]", "Probability that site 1 is conditionally dependent on site 2"], + ["P [Site 1 <–> Site 2]", "Probability that sites 1 and 2 are not conditionally independent"], + ["Site 1 subs", "Substitution counts inferred for Site 1"], + ["Site 2 subs", "Substitution counts inferred for Site 2"], + ["Shared subs", "Substitutions shared by both sites"] + ] + }, + "analysis":{ + "authors":"Art FY Poon, Fraser I Lewis, Simon DW Frost and Sergei L Kosakovsky Pond", + "citation":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950", + "contact":"apoon42@uwo.ca", + "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.", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"1.1" + }, + "branch attributes":{ + "0":{ + "Baboon":{ + "models.DNA.GTR.ModelDescription":0 + }, + "Cat":{ + "models.DNA.GTR.ModelDescription":0.7933191636859576 + }, + "Chimp":{ + "models.DNA.GTR.ModelDescription":0 + }, + "Cow":{ + "models.DNA.GTR.ModelDescription":0.8094119333244753 + }, + "Horse":{ + "models.DNA.GTR.ModelDescription":0.2769077630163064 + }, + "Human":{ + "models.DNA.GTR.ModelDescription":0 + }, + "Mouse":{ + "models.DNA.GTR.ModelDescription":0.1094921058577506 + }, + "Node1":{ + "models.DNA.GTR.ModelDescription":0.4820782253393885 + }, + "Node12":{ + "models.DNA.GTR.ModelDescription":0 + }, + "Node2":{ + "models.DNA.GTR.ModelDescription":0.08259105925424247 + }, + "Node3":{ + "models.DNA.GTR.ModelDescription":0.2526911684326281 + }, + "Node8":{ + "models.DNA.GTR.ModelDescription":0.06531857233184223 + }, + "Node9":{ + "models.DNA.GTR.ModelDescription":0.03361817454867485 + }, + "Pig":{ + "models.DNA.GTR.ModelDescription":0 + }, + "Rat":{ + "models.DNA.GTR.ModelDescription":0.0888784436278628 + }, + "RhMonkey":{ + "models.DNA.GTR.ModelDescription":0 + } + }, + "attributes":{ + "models.DNA.GTR.ModelDescription":{ + "attribute type":"branch length", + "display order":0 + } + } + }, + "data partitions":{ + "0":{ + "coverage": [ +[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] + ], + "name":"bgm.filter.default" + } + }, + "fits":{ + "models.DNA.GTR.ModelDescription":{ + "AIC-c":472.7691802214979, + "Log Likelihood":-210.2027719289308, + "Rate Distributions":null, + "display order":0, + "estimated parameters":24 + } + }, + "input":{ + "datatype":"nucleotide", + "file name":"/tmp/tmpSz4m4X/job_working_directory/000/3/working/bgm_input.fa", + "number of sequences":10, + "number of sites":30, + "trees":{ + "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)" + } + }, + "settings":{ + "burn-in":10000, + "data-type":"nucleotide", + "max-parents":1, + "min-subs":1, + "samples":100, + "steps":100000, + "threshold":0.5 + }, + "tested":0, + "timers":{ + "Baseline fit":{ + "order":1, + "timer":0 + }, + "Network inference":{ + "order":2, + "timer":1 + }, + "Overall":{ + "order":0, + "timer":1 + } + } +} \ No newline at end of file