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feat!: change rulename generate_pgx_report. Update HTML report with clinical recommendations #69

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merged 5 commits into from
Mar 4, 2024
Merged

feat!: change rulename generate_pgx_report. Update HTML report with clinical recommendations #69

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fddfdce
dynamic clinical recommendations without hardcoded genes
chels0 Feb 21, 2024
1988149
feat: generate_pgx_report generates html report and depth table
chels0 Feb 21, 2024
62ecd3a
fix: only color table row with non wildtype haplotype in report
chels0 Feb 27, 2024
9b2eb4b
feat: remove rule generate_depth_report and move templates to config dir
chels0 Feb 27, 2024
7e74e60
Merge pull request #19 from Genomic-Medicine-Linkoping/update_reporting
chels0 Mar 4, 2024
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6 changes: 3 additions & 3 deletions .tests/integration/config/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -78,8 +78,8 @@ reference:
fai: "reference/hg19.chr6.fasta.fai"
dbsnp: "reference/dbsnp_138.sub.vcf.gz"

generate_pgx_report:
report_template: "reference/report_template.txt"
get_clinical_recommendations:
analysed_variants: "reference/analysed_variants.txt"

generate_depth_report:
generate_pgx_report:
html_template: "reference/html_template.html"
6 changes: 6 additions & 0 deletions .tests/integration/reference/analysed_variants.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
Analyserade varianter:
DPYD= rs3918290: c.1905+1G>A, splice defect; rs72549303: c.1898delC, p.P633Qfs; rs72549309: c.299delTCAT; rs1801266: c.703C>T, p.R235W; rs1801268: c.2983G>T, p.V995F; rs78060119: c.1156G>T, p.E386X; rs55886062: c.1679T>G, p.I560S; rs75017182: c.1129-5923C>G; rs67376798: c.2846A>T, p.D949V; rs115232898: c.557A>G, p.Y186C. Dessa varianter motsvarar allelerna *2A, *3, *7, *8, *10, *12, *13, HapB3.

TPMT= rs1800462: c.238G>C, p.A80P; rs1142345: c.719A>G, p.Y240C; rs1800460: c.460G>A, p.A154T; rs1800584: c.626-1G>A. Dessa varianter motsvarar allelerna *2, *3A, *3B, *3C, *4.

NUDT15= rs147390019: c.7974G>A, p.R139H; rs186364861: c.52G>A, p.V18I; rs116855232: c. 7973C>T, p.R139C; rs746071566: c.50delGAGTCG, p.del17_18GV / c.55_56insGAGTCG, p.V18_V19insGV. Dessa varianter motsvarar allelerna *2, *3, *4, *5, *6, *9.
126 changes: 107 additions & 19 deletions .tests/integration/reference/html_template.html
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Expand Up @@ -4,32 +4,64 @@
<meta charset="utf-8">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />



<title>Farmakogenomisk analys av {{sample}}</title>

<style type="text/css">

</script>
<style type="text/css">
.collapsible {
background-color: #fcfcfc;
color: white;
cursor: pointer;
padding: 18px;
width: 100%;
border: none;
text-align: left;
outline: none;
}

.active, .collapsible:hover {
background-color: #edf0f2;
}

.collapsible:after {
content: '\002B';
color: #179bd7;
font-weight: bold;
float: right;
margin-left: 5px;
}

.active:after {
content: "\2212";
}

.content {
max-height: 0;
overflow: hidden;
transition: max-height 0.2s ease-out;
}
</style>


<style type="text/css">
.pagedtable-index-current {
font-weight: bold;
}
#main a.anchor-section {
color: #BBB;
}

h1,h2,h3,h4,h5,h6,legend{
h1,h2,h3,h4,h5,h6,legend, .collapsible{
font-family:"Roboto Slab","ff-tisa-web-pro","Georgia",Arial,sans-serif;
font-weight:700;
color: #9F2042;
}
h1{
h1, .collapsible{
font-size:2rem;
margin-top: 1em;
margin-bottom: 1.2em;
}
h1.title {
h1.title, .collapsible {
margin-top: 1em;
}
h1.title,
Expand Down Expand Up @@ -481,7 +513,7 @@
</style>

</style>
<style type="text/css">h1, h2, h3, h4, h5, h6, legend {
<style type="text/css">h1, h2, h3, h4, h5, h6, legend, .collapsible {
color: #179bd7;
}
#sidebar h2 {
Expand Down Expand Up @@ -593,11 +625,13 @@ <h2><a href="#content">Farmakogenomisk analys av {{sample}}</a></h2>
<div id="toc">
<ul>
<li><a href="#provdetaljer">Provdetaljer</a></li>
<li><a href="#läsdjup-vid-vildtyp-kliniska-targets">Läsdjup vid
vildtyp kliniska targets</a></li>
<li><a href="#läsdjup-vid-targets">Läsdjup vid targets</a></li>
<li><a href="#Kliniska-rekommendationer">Kliniska rekommendationer</a></li>
<li><a href="#Detekterade-varianter">Detekterade varianter</a></li>
<li><a href="#läsdjup-vid-vildtyp-kliniska-targets">Läsdjup för kliniska positioner</a></li>
<li><a href="#Analyserade-varianter">Analyserde varianter</a></li>
<li><a href="#Haplotype">Haplotyper</a></li>
</ul>
</div>
</div>
</div>
<!-- Don't indent these lines or it will mess pre blocks indentation -->
<div id="main">
Expand Down Expand Up @@ -639,22 +673,76 @@ <h1>Provdetaljer</h1>

</tbody>
</table>

<div id="Kliniska-rekommendationer" class="section level1">
<button class="collapsible">Kliniska rekommendationer <span style="color:#f00; font-size:3rem"> {{ warning_rec }}</span></button>
<div class="content">
{{ rekommendation }}
</div>
</div>
<button class="collapsible">Detekterade varianter <span style="color:#f00; font-size:3rem"> {{ warning_rec }}</span></button>
<div class="content">
<div id="Detekterade-varianter" class="section level1" style="overflow:auto;">
<tbody>
<tr>
<td style="text-align:left;width: 15em;border-right:1px solid; overflow-x:auto;">
{{ detected_variants }}
</td>
</tr>
</tbody>
</div>
</div>

<div id="läsdjup-vid-vildtyp-kliniska-targets" class="section level1">
<h1>Läsdjup för kliniska positioner</h1>

<button class="collapsible">Läsdjup för kliniska positioner <span style="color:#f00; font-size:3rem"> {{ warning_depth }}</span> </button>
<div class="content">
{{ table }}
</td>
</tr>
</tbody>
</table>
</div>
</div>

<div id="Analyserade-varianter" class="section level1">
<button class="collapsible">Analyserade varianter</button>
<div class="content">
<table class="table table-striped" style="margin-left: auto; margin-right: auto;">
<tbody>
<tr>
<td style="text-align:left;width: 15em;border-right:1px solid;">
{{ analysed_variants }}
</td>
</tr>
</tbody>
</table>
</div>
<div id="läsdjup-vid-targets" class="section level1">
<h1>Läsdjup vid targets</h1>

</div>

<div id="Haplotype" class="section level1">
<button class="collapsible">Haplotyper</button>
<div class="content">
{{ haplotype_definitions }}

</div>


<script>
var coll = document.getElementsByClassName("collapsible");
var i;

for (i = 0; i < coll.length; i++) {
coll[i].addEventListener("click", function() {
this.classList.toggle("active");
var content = this.nextElementSibling;
if (content.style.maxHeight){
content.style.maxHeight = null;
} else {
content.style.maxHeight = content.scrollHeight + "px";
}
});
}
</script>


</body>
</html>
</html>
8 changes: 4 additions & 4 deletions config/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -81,8 +81,8 @@ get_clinical_guidelines:
get_interaction_guidelines:
interaction_guidelines: "data/guidelines/interaction_guidelines.csv"

generate_pgx_report:
report_template: "data/templates/report_template.txt"
get_clinical_recommendations:
analysed_variants: "config/templates/analysed_variants.txt"

generate_depth_report:
html_template: "data/templates/html_template.html"
generate_pgx_report:
html_template: "config/templates/html_template.html"
10 changes: 5 additions & 5 deletions config/output_files.yaml
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Expand Up @@ -21,22 +21,22 @@ files:
- N

- name: "_copy_pgx_report"
input: "pgx/generate_pgx_report/{sample}_{type}_pgx_report.txt"
output: "results/dna/pgx/{sample}_{type}.pgx_report.txt"
input: "pgx/get_clinical_recommendations/{sample}_{type}_pgx_clinical_recommendations.txt"
output: "results/dna/pgx/{sample}_{type}.pgx_clinical_recommendations.txt"
types:
- T
- N

- name: "_copy_pgx_depth_excel"
input: "pgx/generate_depth_report/{sample}_{type}_pgx_depth.xlsx"
input: "pgx/generate_pgx_report/{sample}_{type}_pgx_depth_table.xlsx"
output: "results/dna/pgx/{sample}_{type}.pgx_depth_table.xlsx"
types:
- T
- N

- name: "_copy_pgx_depth_html"
input: "pgx/generate_depth_report/{sample}_{type}_pgx_depth.html"
output: "results/dna/pgx/{sample}_{type}.pgx_depth_table.html"
input: "pgx/generate_pgx_report/{sample}_{type}_pgx_report.html"
output: "results/dna/pgx/{sample}_{type}.pgx_report.html"
types:
- T
- N
6 changes: 6 additions & 0 deletions config/templates/analysed_variants.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
Analyserade varianter:
DPYD= rs3918290: c.1905+1G>A, splice defect; rs72549303: c.1898delC, p.P633Qfs; rs72549309: c.299delTCAT; rs1801266: c.703C>T, p.R235W; rs1801268: c.2983G>T, p.V995F; rs78060119: c.1156G>T, p.E386X; rs55886062: c.1679T>G, p.I560S; rs75017182: c.1129-5923C>G; rs67376798: c.2846A>T, p.D949V; rs115232898: c.557A>G, p.Y186C. Dessa varianter motsvarar allelerna *2A, *3, *7, *8, *10, *12, *13, HapB3.

TPMT= rs1800462: c.238G>C, p.A80P; rs1142345: c.719A>G, p.Y240C; rs1800460: c.460G>A, p.A154T; rs1800584: c.626-1G>A. Dessa varianter motsvarar allelerna *2, *3A, *3B, *3C, *4.

NUDT15= rs147390019: c.7974G>A, p.R139H; rs186364861: c.52G>A, p.V18I; rs116855232: c. 7973C>T, p.R139C; rs746071566: c.50delGAGTCG, p.del17_18GV / c.55_56insGAGTCG, p.V18_V19insGV. Dessa varianter motsvarar allelerna *2, *3, *4, *5, *6, *9.
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