Mercurial > repos > iuc > hyphy_fade
diff test-data/prime-out1.json @ 8:c257fa0a98a7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
| author | iuc |
|---|---|
| date | Fri, 27 Mar 2020 13:16:39 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-out1.json Fri Mar 27 13:16:39 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, 1.725573110573239, 1, -7.53079217870133, -0.2671292981572289, 1, -7.530980113687253, -0.4804669617756561, 1, -7.530833122267245, -0.1532486612226931, 1, -7.530868793694735], + [10.63135649145974, 0, 0.7502380884715356, -7.750335490678291, -7.750335610925491, 1, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839], + [0, 2.202981274414969, 0.397462976308795, -6.144243972107117, -7.361850215781605, 1, -2.763157788623757, 1, -6.146863972828472, -0.02286865932396898, 1, -6.141696705195292, 2.56489740323532, 1, -6.144140070703968, 3.673465169891661, 1, -6.162164086824393, -0.3782299185469108, 1, -6.140399389962398], + [0, 6.509531966707992, 0.7279903564537584, -7.452295439546786, -8.507460649598423, 1, 6.763405786911178, 1, -7.454926555248795, 0.6678772051425989, 1, -7.451746683657063, -0.5798067642619018, 1, -7.452771449125621, -0.2211171350169704, 1, -7.452165845137638, 0.1663073214171773, 1, -7.450195387750036], + [8.776439958358919, 2.284512411822656, 1.336576511778388, -9.655786100846457, -10.49206003395885, 1, 5.383393783342485, 1, -9.664210115841298, -3.158949692311737, 1, -9.655544560079083, -0.3018714845472609, 1, -9.655318226877892, 3.597509240461804, 1, -9.653746338822806, -0.0948988112495659, 1, -9.655669896512631], + [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, 2.425089497235808, 0.5977083182449383, -7.256204136892792, -8.1869045859499, 1, 5.146566146987978, 1, -7.264970053927162, -2.513623140671756, 1, -7.255847818578761, -0.3554384584781068, 1, -7.256424962957591, 4.119925682148564, 1, -7.254165622670933, -0.1223190226259517, 1, -7.255886801654065], + [6.419869332267623, 0, 0.4530400706576413, -5.863592599386944, -5.863592751403759, 1, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021], + [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, 2.699658477079707, 0.4801615193392039, -5.903524182207455, -6.898872136243598, 1, -0.8716130556024849, 1, -5.903538930457988, -0.4627800379305517, 1, -5.903694932983693, 3.044105631862708, 1, -5.908943461477226, -0.07628230444039112, 1, -5.903502621374115, 0.3057953308962, 1, -5.903488680659473], + [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, 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], + [5.437286509277304, 0, 0.3837007479214133, -9.641801767536267, -9.641801993340092, 1, -0.06122935182163709, 1, -9.641801767535474, -0.06122935182163709, 1, -9.641801767535474, -0.06122935182163709, 1, -9.641801767535474, -0.06122935182163709, 1, -9.641801767535474, -0.06122935182163709, 1, -9.641801767535474], + [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], + [2.976165780520339, 0, 0.2100233331415074, -6.510110085668789, -6.510110085669312, 1, -0.06122935182163709, 1, -6.510110085668789, -0.06122935182163709, 1, -6.510110085668789, -0.06122935182163709, 1, -6.510110085668789, -0.06122935182163709, 1, -6.510110085668789, -0.06122935182163709, 1, -6.510110085668789], + [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, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0], + [7.811867907041998, 0, 0.5512712183698597, -8.853002619643194, -8.85300270595488, 1, -0.06122935182163709, 1, -8.853002619609974, -0.06122935182163709, 1, -8.853002619609974, -0.06122935182163709, 1, -8.853002619609974, -0.06122935182163709, 1, -8.853002619609974, -0.06122935182163709, 1, -8.853002619609974], + [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, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0], + [5.250193239862218, 0, 0.370497870478199, -7.813932328397811, -7.813933401024069, 1, -0.06122935182163709, 1, -7.81393232835335, -0.06122935182163709, 1, -7.81393232835335, -0.06122935182163709, 1, -7.81393232835335, -0.06122935182163709, 1, -7.81393232835335, -0.06122935182163709, 1, -7.81393232835335], + [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], + [7.592268336906083, 0, 0.5357744224661302, -5.63867473098278, -5.638674842181149, 1, -0.06122935182163709, 1, -5.638674730981298, -0.06122935182163709, 1, -5.638674730981298, -0.06122935182163709, 1, -5.638674730981298, -0.06122935182163709, 1, -5.638674730981298, -0.06122935182163709, 1, -5.638674730981298] + ] + }, + "headers": [ +["alpha;", "Synonymous substitution 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 GTR":0.007985902570718373, + "original name":"GOOSE_SHANTOU_2216_2005" + }, + "HONGKONG_1_538_97":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"HONGKONG_1_538_97" + }, + "HONGKONG_1_97_98":{ + "Global MG94xREV":0.02020234274992877, + "Nucleotide GTR":0.02001220163799822, + "original name":"HONGKONG_1_97_98" + }, + "HUMAN_VIETNAM_3062_2004":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"HUMAN_VIETNAM_3062_2004" + }, + "HUMAN_VIETNAM_CL105_2005":{ + "Global MG94xREV":0.006025788919462983, + "Nucleotide GTR":0.005802088014335368, + "original name":"HUMAN_VIETNAM_CL105_2005" + }, + "MALLARD_VIETNAM_16_2003":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"MALLARD_VIETNAM_16_2003" + }, + "Node10":{ + "Global MG94xREV":0, + "Nucleotide GTR":0 + }, + "Node11":{ + "Global MG94xREV":0, + "Nucleotide GTR":0 + }, + "Node13":{ + "Global MG94xREV":0, + "Nucleotide GTR":0 + }, + "Node17":{ + "Global MG94xREV":0, + "Nucleotide GTR":0 + }, + "Node18":{ + "Global MG94xREV":0, + "Nucleotide GTR":0 + }, + "Node19":{ + "Global MG94xREV":0.004922199772633382, + "Nucleotide GTR":0.005534464552270369 + }, + "Node2":{ + "Global MG94xREV":0.006872306486383904, + "Nucleotide GTR":0.006718147482064949 + }, + "Node23":{ + "Global MG94xREV":0, + "Nucleotide GTR":0 + }, + "Node24":{ + "Global MG94xREV":0, + "Nucleotide GTR":0 + }, + "Node25":{ + "Global MG94xREV":0.0008268367968756879, + "Nucleotide GTR":0.0009189593587976459 + }, + "Node3":{ + "Global MG94xREV":0, + "Nucleotide GTR":0 + }, + "Node4":{ + "Global MG94xREV":0.002648185777377607, + "Nucleotide GTR":0.00251461257430795 + }, + "Node5":{ + "Global MG94xREV":0.003268514528883674, + "Nucleotide GTR":0.003965274251091903 + }, + "Node7":{ + "Global MG94xREV":0.005023432525711092, + "Nucleotide GTR":0.004793454999477672 + }, + "Node9":{ + "Global MG94xREV":0.01391813691986412, + "Nucleotide GTR":0.01351408611669037 + }, + "PEREGRINEFALCON_HK_D0028_2004":{ + "Global MG94xREV":0.006920710269269024, + "Nucleotide GTR":0.006722811033712868, + "original name":"PEREGRINEFALCON_HK_D0028_2004" + }, + "SWINE_ANHUI_1_2004":{ + "Global MG94xREV":0.01018798286684916, + "Nucleotide GTR":0.009150633137551082, + "original name":"SWINE_ANHUI_1_2004" + } + }, + "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] + ], + "name":"prime.filter.default" + } + }, + "fits":{ + "Global MG94xREV":{ + "AIC-c":647.6795207053656, + "Equilibrium frequencies": [ +[0.04488063522282697], + [0.02743154763030629], + [0.03260676907658289], + [0.05361444334761576], + [0.01878621141548667], + [0.0114823431236735], + [0.01364859597925394], + [0.02244202343953587], + [0.00898846188937465], + [0.005493848721556544], + [0.006530315351495689], + [0.01073762388516669], + [0.04007728102844568], + [0.02449568367218243], + [0.02911702655775225], + [0.04787635251947601], + [0.02154103095825152], + [0.01316611972632322], + [0.01565003299619046], + [0.02573293310637029], + [0.009016680795182521], + [0.005511096433290134], + [0.006550817007515099], + [0.01077133421300087], + [0.004314126457096238], + [0.002636842477907016], + [0.003134307802358531], + [0.005153658975191914], + [0.01923560009946569], + [0.01175701452767408], + [0.01397508674685076], + [0.02297886352699522], + [0.03843194498464033], + [0.02349003582808618], + [0.02792165371671785], + [0.04591083274306419], + [0.01608690786137961], + [0.00983249851595989], + [0.0116874925496928], + [0.01921743321791434], + [0.00769695150511784], + [0.004704463089092132], + [0.005592004637968804], + [0.00919478452948895], + [0.03431876246786721], + [0.02097601254029597], + [0.02493333610872543], + [0.04099722156245031], + [0.006131000492593795], + [0.01198292502502543], + [0.004198752217504174], + [0.002566324448628536], + [0.003050485878513492], + [0.005015832814718212], + [0.001227885122343091], + [0.001459537288103269], + [0.002399878352343215], + [0.008957344771016727], + [0.00547482958980595], + [0.006507708080284218], + [0.01070045135026252] + ], + "Log Likelihood":-277.7176481414617, + "Rate Distributions":{ + "non-synonymous/synonymous rate ratio for *test*": [ +[0.4074296362572946, 1] + ] + }, + "display order":1, + "estimated parameters":43 + }, + "Nucleotide GTR":{ + "AIC-c":658.4548031196325, + "Equilibrium frequencies": [ +[0.3543689320388349], + [0.1790722761596548], + [0.2076591154261057], + [0.2588996763754045] + ], + "Log Likelihood":-292.5311130078037, + "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, + "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":{ + "0":"(((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516)Node7:0.002095219592954275)Node5:0.003887237703073042)Node4:0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1)Node13:0.002899766890966483)Node11:0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716)Node10:0.000182535836694054,HONGKONG_1_538_97:-1)Node9:0.02096173714686362)Node3:0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651)Node19:0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232)Node18:0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774)Node17:0.004655295319725731)Node2:0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001)Node25:0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184)Node24:0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072)Node23:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)" + } + }, + "tested":{ + "0":{ + "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