Mercurial > repos > iuc > hyphy_fel
diff test-data/prime-out1.json @ 9:8389039f7fbc draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
| author | iuc |
|---|---|
| date | Fri, 27 Mar 2020 13:19:17 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-out1.json Fri Mar 27 13:19:17 2020 -0400 @@ -0,0 +1,391 @@ +{ + "MLE":{ + "content":{ + "0": [ +[0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0], + [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0], + [0, 4.123712641737602, 511.6499971244988, -5.608842688620929, -7.031699805798055, 1, 3.180962375542725, 1, -5.599238755695894, 0.7828049218517579, 1, -5.608352884924835, -2.115291881920681, 1, -5.604784076919627, -5.404956845857691, 1, -5.615111503355894, 2.462902938936584, 1, -5.607953657572869], + [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0], + [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0], + [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0], + [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0], + [0, 4.849174446703908, 0.2440623951294166, -7.530855366772653, -8.547881040478554, 1, 8.833984038052169, 1, -7.53445935473729, 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rate at a site"], + ["β", "Log of property independent non-synonymous rate a site"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"], + ["PRIME LogL", "Site Log-likelihood under the PRIME model"], + ["FEL LogL", "Site Log-likelihood under the FEL model"], + ["p-value", "Omnibus p-value (any property is important)"], + ["λ1", "Importance for Factor I bipolar"], + ["p1", "p-value for non-zero effect of Factor I bipolar"], + ["LogL1", "Log likelihood when there is no effect of Factor I bipolar"], + ["λ2", "Importance for Factor II secondary structure"], + ["p2", "p-value for non-zero effect of Factor II secondary structure"], + ["LogL2", "Log likelihood when there is no effect of Factor II secondary structure"], + ["λ3", "Importance for Factor III volume"], + ["p3", "p-value for non-zero effect of Factor III volume"], + ["LogL3", "Log likelihood when there is no effect of Factor III volume"], + ["λ4", "Importance for Factor IV composition"], + ["p4", "p-value for non-zero effect of Factor IV composition"], + ["LogL4", "Log likelihood when there is no effect of Factor IV composition"], + ["λ5", "Importance for Factor V charge"], + ["p5", "p-value for non-zero effect of Factor V charge"], + ["LogL5", "Log likelihood when there is no effect of Factor V charge"] + ] + }, + "analysis":{ + "authors":"Sergei L. Kosakovsky Pond", + "citation":"TBD", + "contact":"spond@temple.edu", + "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n At each site, N tests are performed\n A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"0.0.1" + }, + "branch attributes":{ + "0":{ + "CHICKEN_CK_160_2005":{ + "Global MG94xREV":0.006875905528136641, + "Nucleotide GTR":0.006740765844759078, + "original name":"CHICKEN_CK_160_2005" + }, + "CHICKEN_HEBEI_326_2005":{ + "Global MG94xREV":0.03000509055831138, + "Nucleotide GTR":0.02817726192677478, + "original name":"CHICKEN_HEBEI_326_2005" + }, + "CHICKEN_HONGKONG_915_97":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"CHICKEN_HONGKONG_915_97" + }, + "CK_HK_WF157_2003":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"CK_HK_WF157_2003" + }, + "GOOSE_HONGKONG_W355_97":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"GOOSE_HONGKONG_W355_97" + }, + "GOOSE_SHANTOU_2216_2005":{ + "Global MG94xREV":0.008912012248907763, + "Nucleotide 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nucleotide A to nucleotide C":0, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0, + "Substitution rate from nucleotide C to nucleotide G":0, + "Substitution rate from nucleotide C to nucleotide T":1.816257034982832, + "Substitution rate from nucleotide G to nucleotide T":0 + }, + "display order":0, + "estimated parameters":36 + } + }, + "input":{ + "file name":"/Users/sergei/Development/tools-iuc/tools/hyphy/test-data/prime-in1.fa", + "number of sequences":13, + "number of sites":50, + "partition count":1, + "trees":{ + 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"CHICKEN_CK_160_2005":"test", + "CHICKEN_HEBEI_326_2005":"test", + "CHICKEN_HONGKONG_915_97":"test", + "CK_HK_WF157_2003":"test", + "GOOSE_HONGKONG_W355_97":"test", + "GOOSE_SHANTOU_2216_2005":"test", + "HONGKONG_1_538_97":"test", + "HONGKONG_1_97_98":"test", + "HUMAN_VIETNAM_3062_2004":"test", + "HUMAN_VIETNAM_CL105_2005":"test", + "MALLARD_VIETNAM_16_2003":"test", + "Node10":"test", + "Node11":"test", + "Node13":"test", + "Node17":"test", + "Node18":"test", + "Node19":"test", + "Node2":"test", + "Node23":"test", + "Node24":"test", + "Node25":"test", + "Node3":"test", + "Node4":"test", + "Node5":"test", + "Node7":"test", + "Node9":"test", + "PEREGRINEFALCON_HK_D0028_2004":"test", + "SWINE_ANHUI_1_2004":"test" + } + }, + "timers":{ + "Model fitting":{ + "order":1, + "timer":3 + }, + "PRIME analysis":{ + "order":2, + "timer":86 + }, + "Total time":{ + "order":0, + "timer":89 + } + } +} \ No newline at end of file