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Merge pull request #548 from GavinHuttley/develop
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MAINT: refactor of Table
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@GavinHuttley
GavinHuttley committed Mar 2, 2020
2 parents e15b8a9 + 87683b8 commit 1917865
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Showing 64 changed files with 7,016 additions and 5,633 deletions.
12 changes: 5 additions & 7 deletions doc/app/available-apps.ipynb
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" hypothesis_result. aligned, serialisable result, hypothesis_result, serialisable ArrayAlignment, Alignment\n",
" cogent3.app.evo model True Define a substitution model + tree for maximum likelihood evaluation.\n",
" Returns model_result. aligned, serialisable result, model_result, serialisable ArrayAlignment, Alignment\n",
" cogent3.app.evo natsel_neutral True Test of selective neutrality by assessing whether omega equals 1.\n",
" Under the alternate, there is one omega for all branches and all sites.\n",
" aligned, serialisable result, hypothesis_result, serialisable ArrayAlignment, Alignment\n",
" cogent3.app.evo natsel_neutral True Test of selective neutrality by assessing whether omega equals 1.\n",
" Under the alternate, there is one omega for all branches and all sites. aligned, serialisable result, hypothesis_result, serialisable ArrayAlignment, Alignment\n",
" cogent3.app.evo natsel_sitehet True Test for site-heterogeneity in omega. Under null, there are 2 site-classes,\n",
" omega < 1 and omega = 1. Under the alternate, an additional site-class of\n",
" omega > 1 is added. aligned, serialisable result, hypothesis_result, serialisable ArrayAlignment, Alignment\n",
Expand All @@ -429,12 +428,11 @@
" alternate that a user specified subset of branches have a distinct value\n",
" (or values) of omega.\n",
" aligned, serialisable result, hypothesis_result, serialisable ArrayAlignment, Alignment\n",
" cogent3.app.evo natsel_zhang True The branch by site-class hypothesis test for natural selection of\n",
" cogent3.app.evo natsel_zhang True The branch by site-class hypothesis test for natural selection of\n",
" Zhang et al MBE 22: 2472-2479.\n",
"\n",
" Note: Our implementation is not as parametrically succinct as that of\n",
" Zhang et al, we have 1 additional bin probability.\n",
" aligned, serialisable result, hypothesis_result, serialisable ArrayAlignment, Alignment\n",
" Zhang et al, we have 1 additional bin probability. aligned, serialisable result, hypothesis_result, serialisable ArrayAlignment, Alignment\n",
" cogent3.app.evo tabulate_stats True Extracts all model statistics from model_result as Table. model_result, serialisable result, tabular_result, serialisable model_result\n",
" cogent3.app.io load_aligned True Loads aligned sequences. Returns an Alignment object. aligned, serialisable DataStoreMember, str, Path\n",
" cogent3.app.io load_db True Loads json serialised cogent3 objects from a TinyDB file. \n",
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.1"
"version": "3.7.3"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
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6 changes: 3 additions & 3 deletions doc/app/dstore.ipynb
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"<style>\n",
"tr:last-child {border-bottom: 1px solid #000;} tr > th {text-align: center !important;} tr > td {text-align: left !important;}\n",
"</style>\n",
"<caption style=\"color: rgb(250, 250, 250); background: rgba(30, 140, 200, 1); align=top;\"><span style=\"font-weight: bold;\">Locked db store. Locked to pid=8582, current pid=13845</span><span></span></caption>\n",
"<caption style=\"color: rgb(250, 250, 250); background: rgba(30, 140, 200, 1); align=top;\"><span style=\"font-weight: bold;\">Locked db store. Locked to pid=8582, current pid=77006</span><span></span></caption>\n",
"<thead style=\"background: rgba(161, 195, 209, 0.75); font-weight: bold; text-align: center;\">\n",
"<th>record type</th>\n",
"<th>number</th>\n",
Expand All @@ -243,7 +243,7 @@
"3 rows x 2 columns</p>"
],
"text/plain": [
"Locked db store. Locked to pid=8582, current pid=13845\n",
"Locked db store. Locked to pid=8582, current pid=77006\n",
"=====================\n",
"record type number\n",
"---------------------\n",
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"name": "python",
"nbconvert_exporter": "python",
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"version": "3.8.1"
"version": "3.7.3"
},
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"application/vnd.jupyter.widget-state+json": {
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104 changes: 46 additions & 58 deletions doc/app/evo-ancestral-states.ipynb
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56 changes: 28 additions & 28 deletions doc/app/evo-dt-nuc-model.ipynb
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24 changes: 12 additions & 12 deletions doc/app/evo-extract-model-stats.ipynb
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"</thead>\n",
"<tbody>\n",
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"<td>Galago</td>\n",
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"</tr>\n",
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"</tr>\n",
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"<td style=\"background: rgba(161, 195, 209, 0.25); font-weight: 600;\">Human</td>\n",
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"</tr>\n",
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"name": "python",
"nbconvert_exporter": "python",
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"version": "3.7.3"
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"application/vnd.jupyter.widget-state+json": {
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52 changes: 26 additions & 26 deletions doc/app/evo-hypothesis.ipynb
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"============================================================\n",
"hypothesis key lnL nfp DLC unique_Q\n",
"------------------------------------------------------------\n",
" null 'GTR' -6992.5741 19 True \n",
" alt 'GN' -6987.8834 25 True \n",
" null 'GTR' -6992.5741 19 True None\n",
" alt 'GN' -6987.8834 25 1 None\n",
"------------------------------------------------------------"
]
},
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"============================================\n",
"key lnL nfp DLC unique_Q\n",
"--------------------------------------------\n",
" -6992.5741 19 True \n",
" -6992.5741 19 True None\n",
"--------------------------------------------\n",
"\n",
"1 rows x 5 columns"
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"</thead>\n",
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"<td style=\"background: rgba(161, 195, 209, 0.25); font-weight: 600;\">HowlerMon</td>\n",
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"</tr>\n",
"<tr>\n",
"<td style=\"background: rgba(161, 195, 209, 0.25); font-weight: 600;\">Rhesus</td>\n",
"<td>Rhesus</td>\n",
"<td>edge.3</td>\n",
"<td style=\"font-family: monospace !important;\">0.0215</td>\n",
"</tr>\n",
"<tr>\n",
"<td style=\"background: rgba(161, 195, 209, 0.25); font-weight: 600;\">Orangutan</td>\n",
"<td>Orangutan</td>\n",
"<td>edge.2</td>\n",
"<td style=\"font-family: monospace !important;\">0.0077</td>\n",
"</tr>\n",
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"<td style=\"background: rgba(161, 195, 209, 0.25); font-weight: 600;\">Gorilla</td>\n",
"<td>Gorilla</td>\n",
"<td>edge.1</td>\n",
"<td style=\"font-family: monospace !important;\">0.0025</td>\n",
"</tr>\n",
"<tr>\n",
"<td style=\"background: rgba(161, 195, 209, 0.25); font-weight: 600;\">Human</td>\n",
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"</tr>\n",
"<tr>\n",
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"</tr>\n",
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"</tr>\n",
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"</tr>\n",
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"</tr>\n",
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"</thead>\n",
"<tbody>\n",
"<tr>\n",
"<td style=\"background: rgba(161, 195, 209, 0.25); font-weight: 600;\">Galago</td>\n",
"<td>Galago</td>\n",
"<td>root</td>\n",
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"</tr>\n",
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"<td>root</td>\n",
"<td style=\"font-family: monospace !important;\">0.0450</td>\n",
"</tr>\n",
"<tr>\n",
"<td style=\"background: rgba(161, 195, 209, 0.25); font-weight: 600;\">Rhesus</td>\n",
"<td>Rhesus</td>\n",
"<td>edge.3</td>\n",
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"</tr>\n",
"<tr>\n",
"<td style=\"background: rgba(161, 195, 209, 0.25); font-weight: 600;\">Orangutan</td>\n",
"<td>Orangutan</td>\n",
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"</tr>\n",
"<tr>\n",
"<td style=\"background: rgba(161, 195, 209, 0.25); font-weight: 600;\">Gorilla</td>\n",
"<td>Gorilla</td>\n",
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"<td style=\"font-family: monospace !important;\">0.0025</td>\n",
"</tr>\n",
"<tr>\n",
"<td style=\"background: rgba(161, 195, 209, 0.25); font-weight: 600;\">Human</td>\n",
"<td>Human</td>\n",
"<td>edge.0</td>\n",
"<td style=\"font-family: monospace !important;\">0.0061</td>\n",
"</tr>\n",
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"<td style=\"background: rgba(161, 195, 209, 0.25); font-weight: 600;\">Chimpanzee</td>\n",
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"<td style=\"font-family: monospace !important;\">0.0028</td>\n",
"</tr>\n",
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"</tr>\n",
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"<td style=\"font-family: monospace !important;\">0.0077</td>\n",
"</tr>\n",
Expand Down Expand Up @@ -637,7 +637,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.1"
"version": "3.7.3"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
Expand Down

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