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{%extends "genotypes/base.html"%}
{%from "flash_messages.html" import flash_all_messages%}
{%block title%}Genotypes{%endblock%}
{%block pagetitle%}Genotypes{%endblock%}
{%block contents%}
{{flash_all_messages()}}
<div class="row">
<h2>Genotype Encoding</h2>
<p>
The genotype encoding used for the "{{population.FullName}}" population from
the "{{species.FullName}}" species is as shown in the table below.
</p>
<table class="table">
<thead>
<tr>
<th>Allele Type</th>
<th>Allele Symbol</th>
<th>Allele Value</th>
</tr>
</thead>
<tbody>
{%for row in genocode%}
<tr>
<td>{{row.AlleleType}}</td>
<td>{{row.AlleleSymbol}}</td>
<td>{{row.DatabaseValue if row.DatabaseValue is not none else "NULL"}}</td>
</tr>
{%else%}
<tr>
<td colspan="7" class="text-info">
<span class="glyphicon glyphicon-exclamation-sign"></span>
There is no explicit genotype encoding defined for this population.
</td>
</tr>
{%endfor%}
</tbody>
</table>
{%if genocode | length < 1%}
<div class="col">
<a href="#add-genotype-encoding"
title="Add a genotype encoding system for this population"
class="btn btn-primary not-implemented">
define genotype encoding
</a>
</div>
{%endif%}
</div>
<div class="row">
<h2 class="subheading">Genetic Markers</h2>
<table id="tbl-genetic-markers" class="table compact stripe cell-border"
data-genetic-markers='{{genetic_markers | tojson}}'>
<thead>
<tr>
<th title="">Index</th>
<th title="">Marker Name</th>
<th title="Chromosome">Chr</th>
<th title="Physical location of the marker in megabasepairs">
Location (Mb)</th>
<th title="">Source</th>
<th title="">Source2</th>
</thead>
<tbody>
{%for marker in markers%}
<tr>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
{%endfor%}
</tbody>
</table>
</div>
<div class="row text-danger">
<h3>Some Important Concepts to Consider/Remember</h3>
<ul>
<li>Reference vs. Non-reference alleles</li>
<li>In <em>GenoCode</em> table, items are ordered by <strong>InbredSet</strong></li>
</ul>
<h3>Possible references</h3>
<ul>
<li>https://mr-dictionary.mrcieu.ac.uk/term/genotype/</li>
<li>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363099/</li>
</ul>
</div>
<div class="row">
<h2>Genotype Datasets</h2>
<p>The genotype data is organised under various genotype datasets. You can
click on the link for the relevant dataset to view a little more information
about it.</p>
{%if dataset is not none%}
<table class="table">
<thead>
<tr>
<th>Name</th>
<th>Full Name</th>
</tr>
</thead>
<tbody>
<tr>
<td>{{dataset.Name}}</td>
<td><a href="{{url_for('species.populations.genotypes.view_dataset',
species_id=species.SpeciesId,
population_id=population.Id,
dataset_id=dataset.Id)}}"
title="View details regarding and manage dataset '{{dataset.FullName}}'">
{{dataset.FullName}}</a></td>
</tr>
</tbody>
</table>
{%else%}
<p class="text-warning">
<span class="glyphicon glyphicon-exclamation-sign"></span>
There is no genotype dataset defined for this population.
</p>
<p>
<a href="{{url_for('species.populations.genotypes.create_dataset',
species_id=species.SpeciesId,
population_id=population.Id)}}"
title="Create a new genotype dataset for the '{{population.FullName}}' population for the '{{species.FullName}}' species."
class="btn btn-primary">
create new genotype dataset</a></p>
{%endif%}
</div>
<div class="row text-warning">
<p>
<span class="glyphicon glyphicon-exclamation-sign"></span>
<strong>NOTE</strong>: Currently the GN2 (and related) system(s) expect a
single genotype dataset. If there is more than one, the system apparently
fails in unpredictable ways.
</p>
<p>Fix this to allow multiple datasets, each with a different assembly from
all the rest.</p>
</div>
{%endblock%}
{%block javascript%}
<script type="text/javascript">
$(function() {
var dtGeneticMarkers = buildDataTable(
"#tbl-genetic-markers",
JSON.parse($("#tbl-genetic-markers").attr("data-genetic-markers")),
[
{data: 'index'},
{data: 'Name'},
{data: 'Chr'},
{data: 'Mb'},
{data: 'Source'},
{data: 'Source2'}
]);
})
</script>
{%endblock%}
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