Mercurial > repos > iuc > hyphy_bgm

annotate test-data/bgm-out1.json @ 16:26ad9a6b1293 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6cabbd9eb2eea9f5d44fe9836cc5f6d6087a839"
author iuc
date Fri, 30 Oct 2020 16:28:30 +0000
parents cdfa1afd7cb0
children
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40 ],
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41 "headers": [
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42 ["Site 1", "Index of site 1"],
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43 ["Site 2", "Index of site 2"],
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44 ["P [Site 1 –> Site 2]", "Probability that site 2 is conditionally dependent on site 1"],
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45 ["P [Site 2 –> Site 1]", "Probability that site 1 is conditionally dependent on site 2"],
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46 ["P [Site 1 <–> Site 2]", "Probability that sites 1 and 2 are not conditionally independent"],
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47 ["Site 1 subs", "Substitution counts inferred for Site 1"],
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48 ["Site 2 subs", "Substitution counts inferred for Site 2"],
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49 ["Shared subs", "Substitutions shared by both sites"]
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50 ]
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51 },
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52 "analysis":{
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53 "authors":"Art FY Poon, Fraser I Lewis, Simon DW Frost and Sergei L Kosakovsky Pond",
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54 "citation":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950",
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55 "contact":"apoon42@uwo.ca",
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56 "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.",
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57 "requirements":"in-frame codon alignment and a phylogenetic tree",
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58 "version":"1.1"
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59 },
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60 "branch attributes":{
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61 "0":{
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62 "Baboon":{
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63 "models.codon.MG_REV.ModelDescription":0
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64 },
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65 "Cat":{
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66 "models.codon.MG_REV.ModelDescription":0.8288168941011919
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67 },
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68 "Chimp":{
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70 },
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71 "Cow":{
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92 "Node3":{
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98 "Node9":{
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101 "Pig":{
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104 "Rat":{
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107 "RhMonkey":{
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111 "attributes":{
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112 "models.codon.MG_REV.ModelDescription":{
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113 "attribute type":"branch length",
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114 "display order":0
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115 }
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116 }
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117 },
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118 "data partitions":{
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119 "0":{
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120 "coverage": [
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121 [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
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122 ],
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123 "name":"bgm.filter.default"
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124 }
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125 },
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126 "fits":{
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127 "models.codon.MG_REV.ModelDescription":{
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diff changeset
128 "AIC-c":508.3788244913426,
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diff changeset
129 "Log Likelihood":-208.6011769515537,
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diff changeset
130 "Rate Distributions":null,
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diff changeset
131 "display order":0,
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diff changeset
132 "estimated parameters":31
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diff changeset
133 }
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134 },
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135 "input":{
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136 "datatype":"codon",
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diff changeset
137 "file name":"/tmp/tmp_Fhyr9/job_working_directory/000/3/working/./bgm_input.fa",
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diff changeset
138 "number of sequences":10,
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139 "number of sites":10,
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140 "trees":{
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diff changeset
141 "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)"
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142 }
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143 },
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diff changeset
144 "settings":{
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diff changeset
145 "burn-in":10000,
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146 "data-type":"codon",
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147 "max-parents":1,
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diff changeset
148 "min-subs":1,
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diff changeset
149 "samples":100,
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diff changeset
150 "steps":100000,
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diff changeset
151 "threshold":0.5
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diff changeset
152 },
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153 "tested":0,
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154 "timers":{
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diff changeset
155 "Baseline fit":{
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diff changeset
156 "order":1,
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diff changeset
157 "timer":3
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diff changeset
158 },
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159 "Network inference":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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160 "order":2,
1
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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161 "timer":0
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bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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162 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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163 "Overall":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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164 "order":0,
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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165 "timer":3
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bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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166 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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167 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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168 }