1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
|
{%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()}}
{%if dataset is defined and dataset is not none%}
<div class="row">
<h2>Genotype Data</h2>
<div class="row">
<div class="col">
<p>
<a href="{{url_for(
'species.populations.genotypes.add_genotype_records',
species_id=species.SpeciesId, population_id=population.Id,
dataset_id=dataset.Id)}}"
class="btn btn-primary">
Add genotype records
</a>
</p>
</div>
</div>
<div class="table-responsive">
<table id="tbl-genotype-records" class="table compact stripe cell-border">
<thead>
<tr>
<th title="">#</th>
<th title="">Index</th>
<th title="Locus of marker on the chromosome">Locus</th>
<th title="Chromosome">Chr</th>
<th title="Physical location of marker in centimorgans">cM</th>
<th title="Physical location of marker in megabasepairs">Mb</th>
{%for sample in samples%}
<th title="Data for sample {{sample}}">{{sample}}</th>
{%endfor%}
</tr>
</thead>
<tbody>
{%for record in genotype_records%}
<tr>
<td>
<input type="checkbox"
id="chk-geno-record-{{record.Id}}"
name="geno_record_id"
value="{{record.Id}}" />
</td>
<td>{{record.index}}</td>
<td>{{record.Name}}</td>
<td>{{record.Chr}}</td>
<td>{{record.cM}}</td>
<td>{{record.Mb}}</td>
{%for sample in samples%}
<td>{{record.data[sample]}}</td>
{%endfor%}
</tr>
{%else%}
<tr>
<td colspan="6" class="text-info">
There are no records
</td>
</tr>
{%endfor%}
</tbody>
</table>
</div>
</div>
<div class="row">
<h2>Genotype Encoding</h2>
<p>The numerical values in the table above are mapped from the following allele symbols:</p>
<table class="table">
<thead>
<tr>
<th>Allele Type</th>
<th>Allele Symbol</th>
<th>Mapped To</th>
</tr>
</thead>
<tbody>
{%for row in genocode%}
<tr>
<td {%if row.AlleleType == 'mat'%}
title="Maternal allele"
{%elif row.AlleleType == "pat"%}
title="Paternal allele"
{%elif row.AlleleType == "het"%}
title="Heterozygous allele"
{%else%}
title="Unknown allele"
{%endif%}>
{{row.AlleleType}}</td>
<td>{{row.AlleleSymbol}}</td>
<td>{{row.DatabaseValue if row.DatabaseValue is not none}}</td>
</tr>
{%else%}
<tr>
<td colspan="3" class="text-info">
There is no genotype encoding defined for this data.
</td>
</tr>
{%endfor%}
</tbody>
</table>
</div>
{%else%}
<div class="row">
<p>We need to create a dataset to hold the genotype information for this
species/population, before we can proceed to upload the genotype data.</p>
<p>Please click the button below to create the dataset.</p>
<div class="col">
<a href="{{url_for('species.populations.genotypes.create_dataset', species_id=species.SpeciesId, population_id=population.Id)}}"
class="btn btn-primary">create genotype dataset</a>
</div>
</div>
{%endif%}
{%endblock%}
{%block javascript%}
<script type="text/javascript">
$(function() {
var genoRecordsUrl = "{{url_for('species.populations.genotypes.index', species_id=species.SpeciesId, population_id=population.Id)}}";
var dtGenotypeRecords = false;
fetch(genoRecordsUrl, {
method: "POST",
headers: {
"Accept": "application/json",
"Content-Type": "application/json"
},
body: JSON.stringify({})
})
.then(response => response.json())
.then(recordsData => {
var records = recordsData.genotype_records;
var samples = recordsData.samples_order;
var columns = [
{
data: function(record) {
return `<input type="checkbox"`
+ `id="chk-geno-record-` + record.Id + `"`
+ `name="geno_record_id"`
+ `value="` + record.Id + `"`
+ ` />`;
}
},
{data: "index"},
{data: "Name"},
{data: "Chr"},
{data: "cM"},
{data: "Mb"}
].concat(samples.map((sample) => {
return {data: (record) => record.data[sample]};
}));
dtGenotypeRecords = buildDataTable(
"#tbl-genotype-records",
[],
columns,
{
serverSide: true,
ajax: {
url: genoRecordsUrl,
dataSrc: "genotype_records",
recordsTotal: "total_genotype_records",
recordsFiltered: "fetched_genotype_records"
},
paging: true,
scroller: true,
scrollY: "50vh",
scrollCollapse: false,
layout: {
top: "info",
topStart: null,
topEnd: null,
bottom: null,
bottomStart: null,
bottomEnd: null
}
});
});
});
</script>
{%endblock%}
|
