Mercurial > repos > iuc > sarscov2summary

comparison test-data/meme.json @ 0:4ad8b610ea41 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
author iuc
date Mon, 04 May 2020 05:42:35 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:4ad8b610ea41
1 {
2 "MLE":{
3 "content":{
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1234 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
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1259 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
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1267 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
1268 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
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1272 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
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1274 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
1275 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
1276 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
1277 [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0]
1278 ]
1279 },
1280 "headers": [
1281 ["alpha;", "Synonymous substitution rate at a site"],
1282 ["&beta;<sup>-</sup>", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"],
1283 ["p<sup>-</sup>", "Mixture distribution weight allocated to &beta;<sup>-</sup>; loosely -- the proportion of the tree evolving neutrally or under negative selection"],
1284 ["&beta;<sup>+</sup>", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"],
1285 ["p<sup>+</sup>", "Mixture distribution weight allocated to &beta;<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under positive selection"],
1286 ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
1287 ["p-value", "Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> &gt; 0 <emph>and<emph> &beta;<sup>+</sup> &gt; &alpha;"],
1288 ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the &beta;<sup>+</sup> rate"],
1289 ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
1290 ["MEME LogL", "Site Log-likelihood under the MEME model"],
1291 ["FEL LogL", "Site Log-likelihood under the FEL model"]
1292 ]
1293 },
1294 "analysis":{
1295 "authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
1296 "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
1297 "contact":"spond@temple.edu",
1298 "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (&alpha;) and a two-category mixture of non-synonymous\n (&beta;-, with proportion p-, and &beta;+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if &beta;+ > &alpha; at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. 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 ",
1299 "requirements":"in-frame codon alignment and a phylogenetic tree",
1300 "version":"2.1.2"
1301 },
1302 "branch attributes":{
1303 "0":{
1304 "MN988713":{
1305 "Global MG94xREV":0,
1306 "Nucleotide GTR":0,
1307 "original name":"MN988713"
1308 },
1309 "MT263436":{
1310 "Global MG94xREV":0,
1311 "Nucleotide GTR":0,
1312 "original name":"MT263436"
1313 },
1314 "MT263450":{
1315 "Global MG94xREV":0.0002667317765692254,
1316 "Nucleotide GTR":0.0002618728984518801,
1317 "original name":"MT263450"
1318 },
1319 "MT263469":{
1320 "Global MG94xREV":0.0002668305373938125,
1321 "Nucleotide GTR":0.0002619448694224783,
1322 "original name":"MT263469"
1323 },
1324 "MT292570":{
1325 "Global MG94xREV":0,
1326 "Nucleotide GTR":0,
1327 "original name":"MT292570"
1328 },
1329 "MT292573":{
1330 "Global MG94xREV":0.0002669328902874902,
1331 "Nucleotide GTR":0.0002619660280897568,
1332 "original name":"MT292573"
1333 },
1334 "MT293207":{
1335 "Global MG94xREV":0.0002666788134209428,
1336 "Nucleotide GTR":0.000261822110100241,
1337 "original name":"MT293207"
1338 },
1339 "MT345866":{
1340 "Global MG94xREV":0.0002666288605363759,
1341 "Nucleotide GTR":0.0002618185708946051,
1342 "original name":"MT345866"
1343 },
1344 "MT350282":{
1345 "Global MG94xREV":0.0002668310057869027,
1346 "Nucleotide GTR":0.0002618372130039719,
1347 "original name":"MT350282"
1348 },
1349 "MultiSeq0_24":{
1350 "Global MG94xREV":0,
1351 "Nucleotide GTR":0,
1352 "original name":"MultiSeq0_24"
1353 },
1354 "MultiSeq1_15":{
1355 "Global MG94xREV":0,
1356 "Nucleotide GTR":0,
1357 "original name":"MultiSeq1_15"
1358 },
1359 "Node6":{
1360 "EBF site 111 (partition 1)":1,
1361 "EBF site 1122 (partition 1)":1,
1362 "EBF site 474 (partition 1)":1,
1363 "EBF site 528 (partition 1)":1,
1364 "EBF site 556 (partition 1)":1,
1365 "EBF site 614 (partition 1)":1e+26,
1366 "EBF site 65 (partition 1)":1,
1367 "EBF site 66 (partition 1)":1,
1368 "EBF site 665 (partition 1)":1,
1369 "EBF site 67 (partition 1)":1,
1370 "EBF site 74 (partition 1)":1,
1371 "EBF site 824 (partition 1)":1,
1372 "Global MG94xREV":0.0002656572436212131,
1373 "Nucleotide GTR":0.0002620203336538703
1374 }
1375 },
1376 "attributes":{
1377 "EBF site 111 (partition 1)":{
1378 "attribute type":"branch label",
1379 "display order":113
1380 },
1381 "EBF site 1122 (partition 1)":{
1382 "attribute type":"branch label",
1383 "display order":1124
1384 },
1385 "EBF site 474 (partition 1)":{
1386 "attribute type":"branch label",
1387 "display order":476
1388 },
1389 "EBF site 528 (partition 1)":{
1390 "attribute type":"branch label",
1391 "display order":530
1392 },
1393 "EBF site 556 (partition 1)":{
1394 "attribute type":"branch label",
1395 "display order":558
1396 },
1397 "EBF site 614 (partition 1)":{
1398 "attribute type":"branch label",
1399 "display order":616
1400 },
1401 "EBF site 65 (partition 1)":{
1402 "attribute type":"branch label",
1403 "display order":67
1404 },
1405 "EBF site 66 (partition 1)":{
1406 "attribute type":"branch label",
1407 "display order":68
1408 },
1409 "EBF site 665 (partition 1)":{
1410 "attribute type":"branch label",
1411 "display order":667
1412 },
1413 "EBF site 67 (partition 1)":{
1414 "attribute type":"branch label",
1415 "display order":69
1416 },
1417 "EBF site 74 (partition 1)":{
1418 "attribute type":"branch label",
1419 "display order":76
1420 },
1421 "EBF site 824 (partition 1)":{
1422 "attribute type":"branch label",
1423 "display order":826
1424 },
1425 "Global MG94xREV":{
1426 "attribute type":"branch length",
1427 "display order":1
1428 },
1429 "Nucleotide GTR":{
1430 "attribute type":"branch length",
1431 "display order":0
1432 },
1433 "original name":{
1434 "attribute type":"node label",
1435 "display order":-1
1436 }
1437 }
1438 },
1439 "data partitions":{
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1443 ],
1444 "name":"meme.filter.default"
1445 }
1446 },
1447 "fits":{
1448 "Global MG94xREV":{
1449 "AIC-c":10149.61287436398,
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1502 [0.0103650227455254],
1503 [0.007720317146018015],
1504 [0.03018440962574672],
1505 [0.00721976906124565],
1506 [0.005377596194652617],
1507 [0.02102498683295317],
1508 [0.02434809464399112],
1509 [0.01239965041937913],
1510 [0.009235795819038476],
1511 [0.03610953267190635]
1512 ],
1513 "Log Likelihood":-5046.748329267292,
1514 "Rate Distributions":{
1515 "non-synonymous/synonymous rate ratio for *background*": [
1516 [0.1425553249428705, 1]
1517 ],
1518 "non-synonymous/synonymous rate ratio for *test*": [
1519 [17.33115892688824, 1]
1520 ]
1521 },
1522 "display order":1,
1523 "estimated parameters":28
1524 },
1525 "Nucleotide GTR":{
1526 "AIC-c":10521.28687405917,
1527 "Equilibrium frequencies": [
1528 [0.294020328977124],
1529 [0.1892451617510534],
1530 [0.1841629174700659],
1531 [0.3325715918017568]
1532 ],
1533 "Log Likelihood":-5233.625428883045,
1534 "Rate Distributions":{
1535 "Substitution rate from nucleotide A to nucleotide C":0,
1536 "Substitution rate from nucleotide A to nucleotide G":1,
1537 "Substitution rate from nucleotide A to nucleotide T":0.1847804107859,
1538 "Substitution rate from nucleotide C to nucleotide G":0,
1539 "Substitution rate from nucleotide C to nucleotide T":0.5743828140832303,
1540 "Substitution rate from nucleotide G to nucleotide T":0.2950953831288027
1541 },
1542 "display order":0,
1543 "estimated parameters":27
1544 }
1545 },
1546 "input":{
1547 "file name":"/galaxy-repl/main/jobdir/028/157/28157295/working/./meme_input.fa",
1548 "number of sequences":11,
1549 "number of sites":1273,
1550 "partition count":1,
1551 "trees":{
1552 "0":"(MN988713,MT292573,MT263469,MT350282,MultiSeq0_24,(MT292570,MT293207,MT345866,MT263436,MultiSeq1_15)Node6,MT263450)"
1553 }
1554 },
1555 "tested":{
1556 "0":{
1557 "MN988713":"background",
1558 "MT263436":"background",
1559 "MT263450":"background",
1560 "MT263469":"background",
1561 "MT292570":"background",
1562 "MT292573":"background",
1563 "MT293207":"background",
1564 "MT345866":"background",
1565 "MT350282":"background",
1566 "MultiSeq0_24":"background",
1567 "MultiSeq1_15":"background",
1568 "Node6":"test"
1569 }
1570 },
1571 "timers":{
1572 "MEME analysis":{
1573 "order":2,
1574 "timer":3
1575 },
1576 "Model fitting":{
1577 "order":1,
1578 "timer":5
1579 },
1580 "Total time":{
1581 "order":0,
1582 "timer":9
1583 }
1584 }
1585 }