Repository 'hyphy_fade'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fade

Changeset 15:a4398cfa8792 (2020-09-18)
Previous changeset 14:a1a03eb66960 (2020-08-21) Next changeset 16:7dbcce65a8ff (2020-10-30)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
modified:
test-data/absrel-out1.json
b
diff -r a1a03eb66960 -r a4398cfa8792 test-data/absrel-out1.json
--- a/test-data/absrel-out1.json Fri Aug 21 15:26:42 2020 -0400
+++ b/test-data/absrel-out1.json Fri Sep 18 21:07:32 2020 +0000
[
b'@@ -1,424 +1,253 @@\n {\n  "analysis":{\n-   "info":"aBSREL (Adaptive branch-site random effects likelihood)\\n                            uses an adaptive random effects branch-site model framework\\n                            to test whether each branch has evolved under positive selection,\\n                            using a procedure which infers an optimal number of rate categories per branch.",\n-   "version":"2.0",\n-   "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353",\n    "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",\n+   "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models",\n    "contact":"spond@temple.edu",\n-   "requirements":"in-frame codon alignment and a phylogenetic tree"\n-  },\n- "input":{\n-   "file name":"/tmp/tmpCAMqUO/job_working_directory/002/2602/working/absrel_input.fa",\n-   "number of sequences":10,\n-   "number of sites":187,\n-   "partition count":1,\n-   "trees":{\n-     "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"\n-    }\n-  },\n- "fits":{\n-   "Nucleotide GTR":{\n-     "Log Likelihood":-3531.96369518556,\n-     "estimated parameters":24,\n-     "AIC-c":7112.577796875186,\n-     "Equilibrium frequencies":[\n-      [0.3563279857397504],\n-      [0.1837789661319073],\n-      [0.2402852049910873],\n-      [0.2196078431372549]\n-      ],\n-     "Rate Distributions":{\n-       "Substitution rate from nucleotide A to nucleotide C":0.5474707834424497,\n-       "Substitution rate from nucleotide A to nucleotide G":1,\n-       "Substitution rate from nucleotide A to nucleotide T":0.2645731370379643,\n-       "Substitution rate from nucleotide C to nucleotide G":0.4867482826410435,\n-       "Substitution rate from nucleotide C to nucleotide T":1.018295973581558,\n-       "Substitution rate from nucleotide G to nucleotide T":0.3026112531229544\n-      },\n-     "display order":0\n-    },\n-   "Baseline MG94xREV":{\n-     "Log Likelihood":-3450.669934819203,\n-     "estimated parameters":46,\n-     "AIC-c":6995.711784065174,\n-     "Equilibrium frequencies":[\n-      [0.04787662253946073],\n-      [0.03913388100305117],\n-      [0.04844580322128512],\n-      [0.0407178971288476],\n-      [0.01817959331488358],\n-      [0.01485982100934833],\n-      [0.01839572120297191],\n-      [0.01546129971531724],\n-      [0.0190238172858878],\n-      [0.01554988139098808],\n-      [0.01924998172104109],\n-      [0.01617929156565557],\n-      [0.02798385246472159],\n-      [0.02287372613761008],\n-      [0.02831653817605838],\n-      [0.02379958245776909],\n-      [0.01680670574479072],\n-      [0.01373763619452979],\n-      [0.01700651207463693],\n-      [0.01429369239710176],\n-      [0.006381800954137531],\n-      [0.005216421415661322],\n-      [0.006457670922102578],\n-      [0.00542756570877943],\n-      [0.006678159032689796],\n-      [0.005458661598138652],\n-      [0.00675755225029668],\n-      [0.00567961101013393],\n-      [0.009823507779659469],\n-      [0.008029638769211124],\n-      [0.009940294440024354],\n-      [0.008354653231583485],\n-      [0.0329096029621651],\n-      [0.02689998621179963],\n-      [0.03330084840219455],\n-      [0.02798881284619018],\n-      [0.01249635346589736],\n-      [0.01021439657952951],\n-      [0.01264491622176376],\n-      [0.01062784315018763],\n-      [0.01307665913959002],\n-      [0.01068873273724336],\n-      [0.0132321208528494],\n-      [0.01112137894012831],\n-      [0.01923563996618058],\n-      [0.01572302316926395],\n-      [0.01946432265285621],\n-      [0.01635944157725275],\n-      [0.01977100255021048],\n-  '..b'\n+      [0.005501589790395056],\n+      [0.009655668202293983],\n+      [0.007888099278638223],\n+      [0.009797203904398108],\n+      [0.008223514024394991],\n+      [0.03326722643528176],\n+      [0.02717732003095303],\n+      [0.03375486749252685],\n+      [0.02833294365668738],\n+      [0.01236215156074466],\n+      [0.01009913314808799],\n+      [0.01254335971371867],\n+      [0.01052856463184265],\n+      [0.01292858539344675],\n+      [0.0105618754683007],\n+      [0.0131180965046964],\n+      [0.01101098350431497],\n+      [0.0193250328267319],\n+      [0.01578738770911659],\n+      [0.0196083049972345],\n+      [0.01645869298147252],\n+      [0.01962343746171723],\n+      [0.02045785777700414],\n+      [0.008926115885166477],\n+      [0.007292098982657142],\n+      [0.009056957588961733],\n+      [0.007602170831388156],\n+      [0.007626222986467745],\n+      [0.009471947420992787],\n+      [0.007950502328516303],\n+      [0.01395367801862353],\n+      [0.01139931439306339],\n+      [0.01415821524731906],\n+      [0.01188403168729233] \n+      ],\n+     "Log Likelihood":-3427.720059001285,\n+     "Rate Distributions":{\n+       "Per-branch delta":{\n+         "2.5%":0,\n+         "97.5%":12.07373117808175,\n+         "Mean":1.277646334033236,\n+         "Median":0.4551223038316586\n+        },\n+       "Per-branch omega":{\n+         "2.5%":0,\n+         "97.5%":2.153434974462683,\n+         "Mean":666666667.5119981,\n+         "Median":1\n+        }\n+      },\n+     "display order":1,\n+     "estimated parameters":62\n+    },\n+   "Full adaptive model":{\n+     "AIC-c":6972.859938351839,\n+     "Log Likelihood":-3415.824749853321,\n+     "Rate Distributions":{\n+      },\n+     "display order":2,\n+     "estimated parameters":68\n+    },\n+   "Nucleotide GTR":{\n+     "AIC-c":7112.857317645923,\n+     "Equilibrium frequencies":      [\n+[0.3592490842490842],\n+      [0.181959706959707],\n+      [0.240018315018315],\n+      [0.2187728937728937] \n+      ],\n+     "Log Likelihood":-3532.321228205235,\n+     "Rate Distributions":{\n+       "Substitution rate from nucleotide A to nucleotide C":0.5498703043473002,\n+       "Substitution rate from nucleotide A to nucleotide G":1,\n+       "Substitution rate from nucleotide A to nucleotide T":0.2646979624678532,\n+       "Substitution rate from nucleotide C to nucleotide G":0.4921328068285813,\n+       "Substitution rate from nucleotide C to nucleotide T":1.028960084526602,\n+       "Substitution rate from nucleotide G to nucleotide T":0.3044365000595399\n+      },\n+     "display order":0,\n+     "estimated parameters":24\n+    }\n+  },\n+ "input":{\n+   "file name":"/tmp/tmpx_42i6f0/job_working_directory/000/6/working/./absrel_input.fa",\n+   "number of sequences":10,\n+   "number of sites":187,\n+   "partition count":1,\n+   "trees":{\n+     "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"\n+    }\n+  },\n+ "test results":{\n+   "P-value threshold":0.05,\n+   "positive test results":0,\n+   "tested":16\n+  },\n+ "tested":{\n+   "0":{\n+     "Baboon":"test",\n+     "Cat":"test",\n+     "Chimp":"test",\n+     "Cow":"test",\n+     "Horse":"test",\n+     "Human":"test",\n+     "Mouse":"test",\n+     "Node1":"test",\n+     "Node12":"test",\n+     "Node2":"test",\n+     "Node3":"test",\n+     "Node8":"test",\n+     "Node9":"test",\n+     "Pig":"test",\n+     "Rat":"test",\n+     "RhMonkey":"test"\n+    }\n+  },\n+ "timers":{\n+   "Baseline model fitting":{\n+     "order":2,\n+     "timer":17\n+    },\n+   "Complexity analysis":{\n+     "order":3,\n+     "timer":110\n+    },\n+   "Full adaptive model fitting":{\n+     "order":4,\n+     "timer":20\n+    },\n+   "Overall":{\n+     "order":0,\n+     "timer":259\n+    },\n+   "Preliminary model fitting":{\n+     "order":1,\n+     "timer":0\n+    },\n+   "Testing for selection":{\n+     "order":5,\n+     "timer":112\n+    }\n   }\n }\n\\ No newline at end of file\n'