Mercurial > repos > iuc > hyphy_fel
comparison 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 |
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date | Fri, 27 Mar 2020 13:19:17 -0400 |
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8:6400b683aced | 9:8389039f7fbc |
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1 { | |
2 "MLE":{ | |
3 "content":{ | |
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55 ] | |
56 }, | |
57 "headers": [ | |
58 ["alpha;", "Synonymous substitution rate at a site"], | |
59 ["β", "Log of property independent non-synonymous rate a site"], | |
60 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"], | |
61 ["PRIME LogL", "Site Log-likelihood under the PRIME model"], | |
62 ["FEL LogL", "Site Log-likelihood under the FEL model"], | |
63 ["p-value", "Omnibus p-value (any property is important)"], | |
64 ["λ1", "Importance for Factor I bipolar"], | |
65 ["p1", "p-value for non-zero effect of Factor I bipolar"], | |
66 ["LogL1", "Log likelihood when there is no effect of Factor I bipolar"], | |
67 ["λ2", "Importance for Factor II secondary structure"], | |
68 ["p2", "p-value for non-zero effect of Factor II secondary structure"], | |
69 ["LogL2", "Log likelihood when there is no effect of Factor II secondary structure"], | |
70 ["λ3", "Importance for Factor III volume"], | |
71 ["p3", "p-value for non-zero effect of Factor III volume"], | |
72 ["LogL3", "Log likelihood when there is no effect of Factor III volume"], | |
73 ["λ4", "Importance for Factor IV composition"], | |
74 ["p4", "p-value for non-zero effect of Factor IV composition"], | |
75 ["LogL4", "Log likelihood when there is no effect of Factor IV composition"], | |
76 ["λ5", "Importance for Factor V charge"], | |
77 ["p5", "p-value for non-zero effect of Factor V charge"], | |
78 ["LogL5", "Log likelihood when there is no effect of Factor V charge"] | |
79 ] | |
80 }, | |
81 "analysis":{ | |
82 "authors":"Sergei L. Kosakovsky Pond", | |
83 "citation":"TBD", | |
84 "contact":"spond@temple.edu", | |
85 "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 ", | |
86 "requirements":"in-frame codon alignment and a phylogenetic tree", | |
87 "version":"0.0.1" | |
88 }, | |
89 "branch attributes":{ | |
90 "0":{ | |
91 "CHICKEN_CK_160_2005":{ | |
92 "Global MG94xREV":0.006875905528136641, | |
93 "Nucleotide GTR":0.006740765844759078, | |
94 "original name":"CHICKEN_CK_160_2005" | |
95 }, | |
96 "CHICKEN_HEBEI_326_2005":{ | |
97 "Global MG94xREV":0.03000509055831138, | |
98 "Nucleotide GTR":0.02817726192677478, | |
99 "original name":"CHICKEN_HEBEI_326_2005" | |
100 }, | |
101 "CHICKEN_HONGKONG_915_97":{ | |
102 "Global MG94xREV":0, | |
103 "Nucleotide GTR":0, | |
104 "original name":"CHICKEN_HONGKONG_915_97" | |
105 }, | |
106 "CK_HK_WF157_2003":{ | |
107 "Global MG94xREV":0, | |
108 "Nucleotide GTR":0, | |
109 "original name":"CK_HK_WF157_2003" | |
110 }, | |
111 "GOOSE_HONGKONG_W355_97":{ | |
112 "Global MG94xREV":0, | |
113 "Nucleotide GTR":0, | |
114 "original name":"GOOSE_HONGKONG_W355_97" | |
115 }, | |
116 "GOOSE_SHANTOU_2216_2005":{ | |
117 "Global MG94xREV":0.008912012248907763, | |
118 "Nucleotide GTR":0.007985902570718373, | |
119 "original name":"GOOSE_SHANTOU_2216_2005" | |
120 }, | |
121 "HONGKONG_1_538_97":{ | |
122 "Global MG94xREV":0, | |
123 "Nucleotide GTR":0, | |
124 "original name":"HONGKONG_1_538_97" | |
125 }, | |
126 "HONGKONG_1_97_98":{ | |
127 "Global MG94xREV":0.02020234274992877, | |
128 "Nucleotide GTR":0.02001220163799822, | |
129 "original name":"HONGKONG_1_97_98" | |
130 }, | |
131 "HUMAN_VIETNAM_3062_2004":{ | |
132 "Global MG94xREV":0, | |
133 "Nucleotide GTR":0, | |
134 "original name":"HUMAN_VIETNAM_3062_2004" | |
135 }, | |
136 "HUMAN_VIETNAM_CL105_2005":{ | |
137 "Global MG94xREV":0.006025788919462983, | |
138 "Nucleotide GTR":0.005802088014335368, | |
139 "original name":"HUMAN_VIETNAM_CL105_2005" | |
140 }, | |
141 "MALLARD_VIETNAM_16_2003":{ | |
142 "Global MG94xREV":0, | |
143 "Nucleotide GTR":0, | |
144 "original name":"MALLARD_VIETNAM_16_2003" | |
145 }, | |
146 "Node10":{ | |
147 "Global MG94xREV":0, | |
148 "Nucleotide GTR":0 | |
149 }, | |
150 "Node11":{ | |
151 "Global MG94xREV":0, | |
152 "Nucleotide GTR":0 | |
153 }, | |
154 "Node13":{ | |
155 "Global MG94xREV":0, | |
156 "Nucleotide GTR":0 | |
157 }, | |
158 "Node17":{ | |
159 "Global MG94xREV":0, | |
160 "Nucleotide GTR":0 | |
161 }, | |
162 "Node18":{ | |
163 "Global MG94xREV":0, | |
164 "Nucleotide GTR":0 | |
165 }, | |
166 "Node19":{ | |
167 "Global MG94xREV":0.004922199772633382, | |
168 "Nucleotide GTR":0.005534464552270369 | |
169 }, | |
170 "Node2":{ | |
171 "Global MG94xREV":0.006872306486383904, | |
172 "Nucleotide GTR":0.006718147482064949 | |
173 }, | |
174 "Node23":{ | |
175 "Global MG94xREV":0, | |
176 "Nucleotide GTR":0 | |
177 }, | |
178 "Node24":{ | |
179 "Global MG94xREV":0, | |
180 "Nucleotide GTR":0 | |
181 }, | |
182 "Node25":{ | |
183 "Global MG94xREV":0.0008268367968756879, | |
184 "Nucleotide GTR":0.0009189593587976459 | |
185 }, | |
186 "Node3":{ | |
187 "Global MG94xREV":0, | |
188 "Nucleotide GTR":0 | |
189 }, | |
190 "Node4":{ | |
191 "Global MG94xREV":0.002648185777377607, | |
192 "Nucleotide GTR":0.00251461257430795 | |
193 }, | |
194 "Node5":{ | |
195 "Global MG94xREV":0.003268514528883674, | |
196 "Nucleotide GTR":0.003965274251091903 | |
197 }, | |
198 "Node7":{ | |
199 "Global MG94xREV":0.005023432525711092, | |
200 "Nucleotide GTR":0.004793454999477672 | |
201 }, | |
202 "Node9":{ | |
203 "Global MG94xREV":0.01391813691986412, | |
204 "Nucleotide GTR":0.01351408611669037 | |
205 }, | |
206 "PEREGRINEFALCON_HK_D0028_2004":{ | |
207 "Global MG94xREV":0.006920710269269024, | |
208 "Nucleotide GTR":0.006722811033712868, | |
209 "original name":"PEREGRINEFALCON_HK_D0028_2004" | |
210 }, | |
211 "SWINE_ANHUI_1_2004":{ | |
212 "Global MG94xREV":0.01018798286684916, | |
213 "Nucleotide GTR":0.009150633137551082, | |
214 "original name":"SWINE_ANHUI_1_2004" | |
215 } | |
216 }, | |
217 "attributes":{ | |
218 "Global MG94xREV":{ | |
219 "attribute type":"branch length", | |
220 "display order":1 | |
221 }, | |
222 "Nucleotide GTR":{ | |
223 "attribute type":"branch length", | |
224 "display order":0 | |
225 }, | |
226 "original name":{ | |
227 "attribute type":"node label", | |
228 "display order":-1 | |
229 } | |
230 } | |
231 }, | |
232 "data partitions":{ | |
233 "0":{ | |
234 "coverage": [ | |
235 [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] | |
236 ], | |
237 "name":"prime.filter.default" | |
238 } | |
239 }, | |
240 "fits":{ | |
241 "Global MG94xREV":{ | |
242 "AIC-c":647.6795207053656, | |
243 "Equilibrium frequencies": [ | |
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297 [0.005015832814718212], | |
298 [0.001227885122343091], | |
299 [0.001459537288103269], | |
300 [0.002399878352343215], | |
301 [0.008957344771016727], | |
302 [0.00547482958980595], | |
303 [0.006507708080284218], | |
304 [0.01070045135026252] | |
305 ], | |
306 "Log Likelihood":-277.7176481414617, | |
307 "Rate Distributions":{ | |
308 "non-synonymous/synonymous rate ratio for *test*": [ | |
309 [0.4074296362572946, 1] | |
310 ] | |
311 }, | |
312 "display order":1, | |
313 "estimated parameters":43 | |
314 }, | |
315 "Nucleotide GTR":{ | |
316 "AIC-c":658.4548031196325, | |
317 "Equilibrium frequencies": [ | |
318 [0.3543689320388349], | |
319 [0.1790722761596548], | |
320 [0.2076591154261057], | |
321 [0.2588996763754045] | |
322 ], | |
323 "Log Likelihood":-292.5311130078037, | |
324 "Rate Distributions":{ | |
325 "Substitution rate from nucleotide A to nucleotide C":0, | |
326 "Substitution rate from nucleotide A to nucleotide G":1, | |
327 "Substitution rate from nucleotide A to nucleotide T":0, | |
328 "Substitution rate from nucleotide C to nucleotide G":0, | |
329 "Substitution rate from nucleotide C to nucleotide T":1.816257034982832, | |
330 "Substitution rate from nucleotide G to nucleotide T":0 | |
331 }, | |
332 "display order":0, | |
333 "estimated parameters":36 | |
334 } | |
335 }, | |
336 "input":{ | |
337 "file name":"/Users/sergei/Development/tools-iuc/tools/hyphy/test-data/prime-in1.fa", | |
338 "number of sequences":13, | |
339 "number of sites":50, | |
340 "partition count":1, | |
341 "trees":{ | |
342 "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)" | |
343 } | |
344 }, | |
345 "tested":{ | |
346 "0":{ | |
347 "CHICKEN_CK_160_2005":"test", | |
348 "CHICKEN_HEBEI_326_2005":"test", | |
349 "CHICKEN_HONGKONG_915_97":"test", | |
350 "CK_HK_WF157_2003":"test", | |
351 "GOOSE_HONGKONG_W355_97":"test", | |
352 "GOOSE_SHANTOU_2216_2005":"test", | |
353 "HONGKONG_1_538_97":"test", | |
354 "HONGKONG_1_97_98":"test", | |
355 "HUMAN_VIETNAM_3062_2004":"test", | |
356 "HUMAN_VIETNAM_CL105_2005":"test", | |
357 "MALLARD_VIETNAM_16_2003":"test", | |
358 "Node10":"test", | |
359 "Node11":"test", | |
360 "Node13":"test", | |
361 "Node17":"test", | |
362 "Node18":"test", | |
363 "Node19":"test", | |
364 "Node2":"test", | |
365 "Node23":"test", | |
366 "Node24":"test", | |
367 "Node25":"test", | |
368 "Node3":"test", | |
369 "Node4":"test", | |
370 "Node5":"test", | |
371 "Node7":"test", | |
372 "Node9":"test", | |
373 "PEREGRINEFALCON_HK_D0028_2004":"test", | |
374 "SWINE_ANHUI_1_2004":"test" | |
375 } | |
376 }, | |
377 "timers":{ | |
378 "Model fitting":{ | |
379 "order":1, | |
380 "timer":3 | |
381 }, | |
382 "PRIME analysis":{ | |
383 "order":2, | |
384 "timer":86 | |
385 }, | |
386 "Total time":{ | |
387 "order":0, | |
388 "timer":89 | |
389 } | |
390 } | |
391 } |