Mercurial > repos > iuc > sarscov2summary
view test-data/prime.json @ 0:4ad8b610ea41 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
author | iuc |
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date | Mon, 04 May 2020 05:42:35 -0400 |
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"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":{ "MN988713":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"MN988713" }, "MT263436":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"MT263436" }, "MT263450":{ "Global MG94xREV":0.0002667176540163485, "Nucleotide GTR":0.0002618730591933583, "original name":"MT263450" }, "MT263469":{ "Global MG94xREV":0.0002667987066023138, "Nucleotide GTR":0.0002619448078896464, "original name":"MT263469" }, "MT292570":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"MT292570" }, "MT292573":{ "Global MG94xREV":0.0002669181767063246, "Nucleotide GTR":0.0002619663648691002, "original name":"MT292573" }, "MT293207":{ "Global MG94xREV":0.0002666526185143277, "Nucleotide GTR":0.0002618218819513519, "original name":"MT293207" }, "MT345866":{ "Global MG94xREV":0.0002666096429981044, "Nucleotide GTR":0.000261818318230699, "original name":"MT345866" }, "MT350282":{ "Global MG94xREV":0.000266810149603764, "Nucleotide GTR":0.0002618371209939757, "original name":"MT350282" }, "MultiSeq0_24":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"MultiSeq0_24" }, "MultiSeq1_15":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"MultiSeq1_15" }, "Node6":{ "Global MG94xREV":0.0002670753253809918, "Nucleotide GTR":0.0002620206108107774 } }, "attributes":{ "Global MG94xREV":{ "attribute type":"branch length", "display order":1 }, "Nucleotide GTR":{ "attribute type":"branch length", "display order":0 }, "original name":{ "attribute type":"node label", "display order":-1 } } }, "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, 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[0.007859327000813585], [0.00400248597545707], [0.00298122463034224], [0.01165580425345982], [0.01349806434457642], [0.006874101717537849], [0.005120128209683852], [0.02001835472486404], [0.0282479035525974], [0.01438568948634293], [0.01071508359657485], [0.0418931588347964], [0.01986646282387325], [0.01011730887724364], [0.007535809145258669], [0.02946303186770731], [0.01383800857688485], [0.007047223668324623], [0.00524907692478322], [0.02052251028786194], [0.02376619908450893], [0.01210331094708498], [0.009015069365738402], [0.0352465502897533], [0.01473791109327413], [0.04291887788275893], [0.02035287659406526], [0.0103650227455254], [0.007720317146018015], [0.03018440962574672], [0.00721976906124565], [0.005377596194652617], [0.02102498683295317], [0.02434809464399112], [0.01239965041937913], [0.009235795819038476], [0.03610953267190635] ], "Log Likelihood":-5046.7483296315, "Rate Distributions":{ "non-synonymous/synonymous rate ratio for *background*": [ [0.1425350635756608, 1] ], "non-synonymous/synonymous rate ratio for *test*": [ [17.44166093270076, 1] ] }, "display order":1, "estimated parameters":28 }, "Nucleotide GTR":{ "AIC-c":10521.28687406032, "Equilibrium frequencies": [ [0.294020328977124], [0.1892451617510534], [0.1841629174700659], [0.3325715918017568] ], "Log Likelihood":-5233.62542888362, "Rate Distributions":{ "Substitution rate from nucleotide A to nucleotide C":0, "Substitution rate from nucleotide A to nucleotide G":1, "Substitution rate from nucleotide A to nucleotide T":0.1847803064876015, "Substitution rate from nucleotide C to nucleotide G":0, "Substitution rate from nucleotide C to nucleotide T":0.5743828140832303, "Substitution rate from nucleotide G to nucleotide T":0.2950953831288027 }, "display order":0, "estimated parameters":27 } }, "input":{ "file name":"/galaxy-repl/main/jobdir/028/157/28157290/working/./prime_input.fa", "number of sequences":11, "number of sites":1273, "partition count":1, "trees":{ "0":"(MN988713,MT292573,MT263469,MT350282,MultiSeq0_24,(MT292570,MT293207,MT345866,MT263436,MultiSeq1_15)Node6,MT263450)" } }, "tested":{ "0":{ "MN988713":"background", "MT263436":"background", "MT263450":"background", "MT263469":"background", "MT292570":"background", "MT292573":"background", "MT293207":"background", "MT345866":"background", "MT350282":"background", "MultiSeq0_24":"background", "MultiSeq1_15":"background", "Node6":"test" } }, "timers":{ "Model fitting":{ "order":1, "timer":7 }, "PRIME analysis":{ "order":2, "timer":58 }, "Total time":{ "order":0, "timer":66 } } }