Mercurial > repos > iuc > hyphy_absrel

comparison test-data/params.json @ 0:419cd817299c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
author iuc
date Thu, 17 Jan 2019 04:22:13 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:419cd817299c
1 {
2 "filepath": "/home/sweaver/datamonkey/datamonkey-js-dev/app/models/../../uploads/msa/5446bc0d355080301f18a8c6.fasta",
3 "msa": [
4 {
5 "rawsites": 1698,
6 "nj": "(((((((TREESPARROW_HENAN_1_2004:0.0111333782927653,TREESPARROW_HENAN_3_2004:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.009062780987312381):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-0.001089936320307174,(GOOSE_HONGKONG_W355_97:-0.002798420018760263,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97:-8.034074555865944e-05):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452)",
7 "goodtree": 0,
8 "sequences": 21,
9 "sites": 566,
10 "partitions": 1,
11 "analysis_type": "1",
12 "gencodeid": 0,
13 "datatype": 0,
14 "_id": "5446bc0d355080301f18a8c7",
15 "created": "2014-10-21T20:03:25.803Z",
16 "sequence_info": [
17 {
18 "seqindex": 0,
19 "name": "TREESPARROW_HENAN_1_2004",
20 "_id": "5446bc0d355080301f18a8c8"
21 },
22 {
23 "seqindex": 1,
24 "name": "HUMAN_VIETNAM_CL105_2005",
25 "_id": "5446bc0d355080301f18a8c9"
26 },
27 {
28 "seqindex": 2,
29 "name": "TREESPARROW_HENAN_4_2004",
30 "_id": "5446bc0d355080301f18a8ca"
31 },
32 {
33 "seqindex": 3,
34 "name": "CHICKEN_HEBEI_326_2005",
35 "_id": "5446bc0d355080301f18a8cb"
36 },
37 {
38 "seqindex": 4,
39 "name": "CHICKEN_HONGKONG_915_97",
40 "_id": "5446bc0d355080301f18a8cc"
41 },
42 {
43 "seqindex": 5,
44 "name": "HUMAN_VIETNAM_3062_2004",
45 "_id": "5446bc0d355080301f18a8cd"
46 },
47 {
48 "seqindex": 6,
49 "name": "GOOSE_HONGKONG_W355_97",
50 "_id": "5446bc0d355080301f18a8ce"
51 },
52 {
53 "seqindex": 7,
54 "name": "DUCK_HONGKONG_Y283_97",
55 "_id": "5446bc0d355080301f18a8cf"
56 },
57 {
58 "seqindex": 8,
59 "name": "DUCK_VIETNAM_376_2005",
60 "_id": "5446bc0d355080301f18a8d0"
61 },
62 {
63 "seqindex": 9,
64 "name": "MALLARD_VIETNAM_16_2003",
65 "_id": "5446bc0d355080301f18a8d1"
66 },
67 {
68 "seqindex": 10,
69 "name": "CHICKEN_CK_160_2005",
70 "_id": "5446bc0d355080301f18a8d2"
71 },
72 {
73 "seqindex": 11,
74 "name": "DUCK_GUANGZHOU_20_2005",
75 "_id": "5446bc0d355080301f18a8d3"
76 },
77 {
78 "seqindex": 12,
79 "name": "CK_HK_WF157_2003",
80 "_id": "5446bc0d355080301f18a8d4"
81 },
82 {
83 "seqindex": 13,
84 "name": "SWINE_ANHUI_1_2004",
85 "_id": "5446bc0d355080301f18a8d5"
86 },
87 {
88 "seqindex": 14,
89 "name": "DUCK_VIETNAM_272_2005",
90 "_id": "5446bc0d355080301f18a8d6"
91 },
92 {
93 "seqindex": 15,
94 "name": "HONGKONG_1_97_98",
95 "_id": "5446bc0d355080301f18a8d7"
96 },
97 {
98 "seqindex": 16,
99 "name": "GOOSE_SHANTOU_2216_2005",
100 "_id": "5446bc0d355080301f18a8d8"
101 },
102 {
103 "seqindex": 17,
104 "name": "TREESPARROW_HENAN_3_2004",
105 "_id": "5446bc0d355080301f18a8d9"
106 },
107 {
108 "seqindex": 18,
109 "name": "PEREGRINEFALCON_HK_D0028_2004",
110 "_id": "5446bc0d355080301f18a8da"
111 },
112 {
113 "seqindex": 19,
114 "name": "TREESPARROW_HENAN_2_2004",
115 "_id": "5446bc0d355080301f18a8db"
116 },
117 {
118 "seqindex": 20,
119 "name": "HONGKONG_1_538_97",
120 "_id": "5446bc0d355080301f18a8dc"
121 }
122 ],
123 "partition_info": [
124 {
125 "partition": 1,
126 "startcodon": 0,
127 "endcodon": 1697,
128 "span": 1698,
129 "_id": "5446bc0d355080301f18a8dd"
130 }
131 ]
132 }
133 ],
134 "analysis": {
135 "status": "In Queue",
136 "tagged_nwk_tree": "(((((((TREESPARROW_HENAN_1_2004{FG}:0.0111333782927653,TREESPARROW_HENAN_3_2004{FG}:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.00906278098731238):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97,(GOOSE_HONGKONG_W355_97,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452)",
137 "_id": "5446bc0d355080301f18a8c6",
138 "__t": "Busted",
139 "mail": "sweaver@ucsd.edu",
140 "analysis_type": 1,
141 "__v": 0,
142 "msa": [
143 {
144 "partition_info": [
145 {
146 "_id": "5446bc0d355080301f18a8dd",
147 "span": 1698,
148 "endcodon": 1697,
149 "startcodon": 0,
150 "partition": 1
151 }
152 ],
153 "sequence_info": [
154 {
155 "_id": "5446bc0d355080301f18a8c8",
156 "name": "TREESPARROW_HENAN_1_2004",
157 "seqindex": 0
158 },
159 {
160 "_id": "5446bc0d355080301f18a8c9",
161 "name": "HUMAN_VIETNAM_CL105_2005",
162 "seqindex": 1
163 },
164 {
165 "_id": "5446bc0d355080301f18a8ca",
166 "name": "TREESPARROW_HENAN_4_2004",
167 "seqindex": 2
168 },
169 {
170 "_id": "5446bc0d355080301f18a8cb",
171 "name": "CHICKEN_HEBEI_326_2005",
172 "seqindex": 3
173 },
174 {
175 "_id": "5446bc0d355080301f18a8cc",
176 "name": "CHICKEN_HONGKONG_915_97",
177 "seqindex": 4
178 },
179 {
180 "_id": "5446bc0d355080301f18a8cd",
181 "name": "HUMAN_VIETNAM_3062_2004",
182 "seqindex": 5
183 },
184 {
185 "_id": "5446bc0d355080301f18a8ce",
186 "name": "GOOSE_HONGKONG_W355_97",
187 "seqindex": 6
188 },
189 {
190 "_id": "5446bc0d355080301f18a8cf",
191 "name": "DUCK_HONGKONG_Y283_97",
192 "seqindex": 7
193 },
194 {
195 "_id": "5446bc0d355080301f18a8d0",
196 "name": "DUCK_VIETNAM_376_2005",
197 "seqindex": 8
198 },
199 {
200 "_id": "5446bc0d355080301f18a8d1",
201 "name": "MALLARD_VIETNAM_16_2003",
202 "seqindex": 9
203 },
204 {
205 "_id": "5446bc0d355080301f18a8d2",
206 "name": "CHICKEN_CK_160_2005",
207 "seqindex": 10
208 },
209 {
210 "_id": "5446bc0d355080301f18a8d3",
211 "name": "DUCK_GUANGZHOU_20_2005",
212 "seqindex": 11
213 },
214 {
215 "_id": "5446bc0d355080301f18a8d4",
216 "name": "CK_HK_WF157_2003",
217 "seqindex": 12
218 },
219 {
220 "_id": "5446bc0d355080301f18a8d5",
221 "name": "SWINE_ANHUI_1_2004",
222 "seqindex": 13
223 },
224 {
225 "_id": "5446bc0d355080301f18a8d6",
226 "name": "DUCK_VIETNAM_272_2005",
227 "seqindex": 14
228 },
229 {
230 "_id": "5446bc0d355080301f18a8d7",
231 "name": "HONGKONG_1_97_98",
232 "seqindex": 15
233 },
234 {
235 "_id": "5446bc0d355080301f18a8d8",
236 "name": "GOOSE_SHANTOU_2216_2005",
237 "seqindex": 16
238 },
239 {
240 "_id": "5446bc0d355080301f18a8d9",
241 "name": "TREESPARROW_HENAN_3_2004",
242 "seqindex": 17
243 },
244 {
245 "_id": "5446bc0d355080301f18a8da",
246 "name": "PEREGRINEFALCON_HK_D0028_2004",
247 "seqindex": 18
248 },
249 {
250 "_id": "5446bc0d355080301f18a8db",
251 "name": "TREESPARROW_HENAN_2_2004",
252 "seqindex": 19
253 },
254 {
255 "_id": "5446bc0d355080301f18a8dc",
256 "name": "HONGKONG_1_538_97",
257 "seqindex": 20
258 }
259 ],
260 "created": "2014-10-21T20:03:25.803Z",
261 "_id": "5446bc0d355080301f18a8c7",
262 "datatype": 0,
263 "gencodeid": 0,
264 "partitions": 1,
265 "sites": 566,
266 "sequences": 21,
267 "goodtree": 0,
268 "nj": "(((((((TREESPARROW_HENAN_1_2004:0.0111333782927653,TREESPARROW_HENAN_3_2004:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.009062780987312381):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-0.001089936320307174,(GOOSE_HONGKONG_W355_97:-0.002798420018760263,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97:-8.034074555865944e-05):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452)",
269 "rawsites": 1698
270 }
271 ],
272 "created": "2014-10-21T20:03:25.798Z"
273 },
274 "status_stack": [
275 "In Queue",
276 "Running",
277 "Completed"
278 ],
279 "type": "relax"
280 }