diff test-data/absrel-out2.json @ 6:81b23515db14 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/absrel-out2.json	Wed Mar 30 00:23:34 2022 +0000
@@ -0,0 +1,535 @@
+{
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+  ],
+ "analysis":{
+   "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
+   "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models. v2.3 adds support for SRV",
+   "contact":"[e-mail]",
+   "info":"aBSREL (Adaptive branch-site random effects likelihood)\n                            uses an adaptive random effects branch-site model framework\n                            to test whether each branch has evolved under positive selection,\n                            using a procedure which infers an optimal number of rate categories per branch.",
+   "requirements":"in-frame codon alignment and a phylogenetic tree",
+   "version":"2.3"
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+       "Rate Distributions":        [
+[0, 1] 
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+       "Rate classes":1,
+       "Uncorrected P-value":1,
+       "original name":"Baboon",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0
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+[10000000000, 1] 
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+       "Uncorrected P-value":0.3081784202350423,
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+       "Rate classes":1,
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+       "Rate classes":1,
+       "Uncorrected P-value":0.393889915055757,
+       "original name":"Horse",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0
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+       "Baseline MG94xREV omega ratio":1,
+       "Corrected P-value":1,
+       "Full adaptive model":0,
+       "Full adaptive model (non-synonymous subs/site)":1e-10,
+       "Full adaptive model (synonymous subs/site)":1e-10,
+       "LRT":0,
+       "Nucleotide GTR":0,
+       "Rate Distributions":        [
+[1, 1] 
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+       "Rate classes":1,
+       "Uncorrected P-value":1,
+       "original name":"Human",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0.0009494209875164728
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+       "Uncorrected P-value":1,
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+       "rate at which 2 nucleotides are changed instantly within a single codon":0.02214869577417109
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+       "Rate classes":1,
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+        ],
+       "Rate classes":1,
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+       "rate at which 2 nucleotides are changed instantly within a single codon":10.77888358494443
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+[1.433858907010162, 1] 
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+       "Rate classes":1,
+       "Uncorrected P-value":0.389355679288724,
+       "rate at which 2 nucleotides are changed instantly within a single codon":0.3287265444712935
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+     "Node8":{
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+       "Full adaptive model (synonymous subs/site)":0.01569223942956148,
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+       "Rate Distributions":        [
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+        ],
+       "Rate classes":1,
+       "Uncorrected P-value":0.2771341436242022,
+       "rate at which 2 nucleotides are changed instantly within a single codon":0.2354207827705045
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+     "Node9":{
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+       "Baseline MG94xREV omega ratio":0.4077675922423373,
+       "Corrected P-value":1,
+       "Full adaptive model":0.03019973043687331,
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+       "Rate Distributions":        [
+[0.4119078417573153, 1] 
+        ],
+       "Rate classes":1,
+       "Uncorrected P-value":1,
+       "rate at which 2 nucleotides are changed instantly within a single codon":0
+      },
+     "Pig":{
+       "Baseline MG94xREV":0.217114312357174,
+       "Baseline MG94xREV omega ratio":1.283370430439691,
+       "Corrected P-value":1,
+       "Full adaptive model":0.2181331361104026,
+       "Full adaptive model (non-synonymous subs/site)":0.1712686263446052,
+       "Full adaptive model (synonymous subs/site)":0.04686450976579729,
+       "LRT":0.5406119303397645,
+       "Nucleotide GTR":0.1871390433004313,
+       "Rate Distributions":        [
+[1.302541757406645, 1] 
+        ],
+       "Rate classes":1,
+       "Uncorrected P-value":0.3213796354214938,
+       "original name":"Pig",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0
+      },
+     "Rat":{
+       "Baseline MG94xREV":0.06785652890791004,
+       "Baseline MG94xREV omega ratio":0.9234518387715737,
+       "Corrected P-value":1,
+       "Full adaptive model":0.06783877994658692,
+       "Full adaptive model (non-synonymous subs/site)":0.04934287026354431,
+       "Full adaptive model (synonymous subs/site)":0.01849590968304254,
+       "LRT":0,
+       "Nucleotide GTR":0.06661490534189227,
+       "Rate Distributions":        [
+[0.939079296251313, 1] 
+        ],
+       "Rate classes":1,
+       "Uncorrected P-value":1,
+       "original name":"Rat",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0.02234985038534893
+      },
+     "RhMonkey":{
+       "Baseline MG94xREV":0.0036869629402653,
+       "Baseline MG94xREV omega ratio":10000000000,
+       "Corrected P-value":1,
+       "Full adaptive model":0.003691831254195047,
+       "Full adaptive model (non-synonymous subs/site)":0.003691831254195047,
+       "Full adaptive model (synonymous subs/site)":1e-10,
+       "LRT":1.049935795353122,
+       "Nucleotide GTR":0.003778804730491441,
+       "Rate Distributions":        [
+[10000000000, 1] 
+        ],
+       "Rate classes":1,
+       "Uncorrected P-value":0.2385766813428075,
+       "original name":"RhMonkey",
+       "rate at which 2 nucleotides are changed instantly within a single codon":0
+      }
+    },
+   "attributes":{
+     "Baseline MG94xREV":{
+       "attribute type":"branch length",
+       "display order":1
+      },
+     "Baseline MG94xREV omega ratio":{
+       "attribute type":"branch label",
+       "display order":1
+      },
+     "Corrected P-value":{
+       "attribute type":"branch label",
+       "display order":6
+      },
+     "Full adaptive model":{
+       "attribute type":"branch length",
+       "display order":2
+      },
+     "Full adaptive model (non-synonymous subs/site)":{
+       "attribute type":"branch label",
+       "display order":10
+      },
+     "Full adaptive model (synonymous subs/site)":{
+       "attribute type":"branch label",
+       "display order":9
+      },
+     "LRT":{
+       "attribute type":"branch label",
+       "display order":4
+      },
+     "Nucleotide GTR":{
+       "attribute type":"branch length",
+       "display order":0
+      },
+     "Rate Distributions":{
+       "attribute type":"branch label",
+       "display order":3
+      },
+     "Rate classes":{
+       "attribute type":"branch label",
+       "display order":2
+      },
+     "Uncorrected P-value":{
+       "attribute type":"branch label",
+       "display order":5
+      },
+     "original name":{
+       "attribute type":"node label",
+       "display order":-1
+      },
+     "rate at which 2 nucleotides are changed instantly within a single codon":{
+       "attribute type":"branch label",
+       "display order":7
+      }
+    }
+  },
+ "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, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186] 
+      ],
+     "name":"absrel.filter.default"
+    }
+  },
+ "fits":{
+   "Baseline MG94xREV":{
+     "AIC-c":6938.369899478594,
+     "Equilibrium frequencies":      [
+[0.04876086397632926],
+      [0.03982224127745371],
+      [0.0494959405650269],
+      [0.04152830682371345],
+      [0.01810345074594235],
+      [0.01478480742075003],
+      [0.01837636270304883],
+      [0.01541821854326533],
+      [0.01892910005547028],
+      [0.01545910240515689],
+      [0.01921445878706794],
+      [0.01612140169177368],
+      [0.02829747763884322],
+      [0.02311011106415996],
+      [0.02872406592369408],
+      [0.02410019507229243],
+      [0.01663805943190806],
+      [0.01358804506433061],
+      [0.01688888041768248],
+      [0.01417018446135155],
+      [0.006177213955434187],
+      [0.005044834822351987],
+      [0.006270336287397383],
+      [0.00526096577332031],
+      [0.006458939937330408],
+      [0.005274916061901906],
+      [0.006556309326397028],
+      [0.005500904159606446],
+      [0.009655594186286731],
+      [0.007885574003572761],
+      [0.009801153568494354],
+      [0.008223407979974132],
+      [0.03327785448210915],
+      [0.02717750758119989],
+      [0.03377952261833742],
+      [0.02834184710178207],
+      [0.01235507229404208],
+      [0.01009019590244688],
+      [0.01254132667213156],
+      [0.01052248035033209],
+      [0.01291855364640413],
+      [0.01055038238273567],
+      [0.01311330258173711],
+      [0.01100238215235291],
+      [0.01931219560697892],
+      [0.0157719705998612],
+      [0.01960332955558842],
+      [0.01644767379420349],
+      [0.01965132601881859],
+      [0.02049322866376102],
+      [0.008933621043463411],
+      [0.007295949736387736],
+      [0.009068296583349953],
+      [0.007608523013862737],
+      [0.007628698224327205],
+      [0.009481877006094248],
+      [0.00795552712159237],
+      [0.01396413011303752],
+      [0.01140428846505027],
+      [0.01417464125436193],
+      [0.01189287130232129] 
+      ],
+     "Log Likelihood":-3399.656647852504,
+     "Rate Distributions":{
+       "Per-branch delta":{
+         "2.5%":0,
+         "97.5%":10.66318587577853,
+         "Mean":1.142287895998736,
+         "Median":0.2080459069952131
+        },
+       "Per-branch omega":{
+         "2.5%":0,
+         "97.5%":2.028136557891868,
+         "Mean":666666667.5178814,
+         "Median":1
+        },
+       "Synonymous site-to-site rates":{
+         "0":{
+           "proportion":0.3499070593950995,
+           "rate":0.3584907731592092
+          },
+         "1":{
+           "proportion":0.5579704535685105,
+           "rate":1.083607309819905
+          },
+         "2":{
+           "proportion":0.09212248703639001,
+           "rate":2.93023662601063
+          }
+        }
+      },
+     "display order":1,
+     "estimated parameters":67
+    },
+   "Full adaptive model":{
+     "AIC-c":6937.867430345418,
+     "Log Likelihood":-3399.405413285916,
+     "Rate Distributions":{
+      },
+     "display order":2,
+     "estimated parameters":67
+    },
+   "Nucleotide GTR":{
+     "AIC-c":7112.857288723968,
+     "Equilibrium frequencies":      [
+[0.3592490842490842],
+      [0.181959706959707],
+      [0.240018315018315],
+      [0.2187728937728937] 
+      ],
+     "Log Likelihood":-3532.321213744258,
+     "Rate Distributions":{
+       "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
+       "Substitution rate from nucleotide A to nucleotide G":1,
+       "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
+       "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
+       "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
+       "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
+      },
+     "display order":0,
+     "estimated parameters":24
+    }
+  },
+ "input":{
+   "file name":"/tmp/tmpasswxnks/job_working_directory/000/9/working/./input.fasta",
+   "number of sequences":10,
+   "number of sites":187,
+   "partition count":1,
+   "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)"
+    }
+  },
+ "runtime":"2.5.36",
+ "test results":{
+   "P-value threshold":0.05,
+   "positive test results":0,
+   "tested":16
+  },
+ "tested":{
+   "0":{
+     "Baboon":"test",
+     "Cat":"test",
+     "Chimp":"test",
+     "Cow":"test",
+     "Horse":"test",
+     "Human":"test",
+     "Mouse":"test",
+     "Node1":"test",
+     "Node12":"test",
+     "Node2":"test",
+     "Node3":"test",
+     "Node8":"test",
+     "Node9":"test",
+     "Pig":"test",
+     "Rat":"test",
+     "RhMonkey":"test"
+    }
+  },
+ "timers":{
+   "Baseline model fitting":{
+     "order":2,
+     "timer":129
+    },
+   "Complexity analysis":{
+     "order":3,
+     "timer":406
+    },
+   "Full adaptive model fitting":{
+     "order":4,
+     "timer":46
+    },
+   "Overall":{
+     "order":0,
+     "timer":1006
+    },
+   "Preliminary model fitting":{
+     "order":1,
+     "timer":0
+    },
+   "Testing for selection":{
+     "order":5,
+     "timer":424
+    }
+  }
+}
\ No newline at end of file