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feat: Display all MMSplice and SpliceAI Scores (#296) #310

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merged 2 commits into from
Dec 18, 2023
Merged

feat: Display all MMSplice and SpliceAI Scores (#296) #310

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6ef4375
wip
gromdimon Dec 15, 2023
c3a4dd2
feat: present all scores
gromdimon Dec 18, 2023
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115 changes: 102 additions & 13 deletions frontend/src/components/SeqvarDetails/VariantScoresCard.vue
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<script setup lang="ts">
import { computed } from 'vue'
import { computed, ref } from 'vue'

import ScoreDisplay from '@/components/SeqvarDetails/VariantScoresCard/ScoreDisplay.vue'
import Conservation from '@/components/SeqvarDetails/VariantScoresCard/UcscConservation.vue'
Expand Down Expand Up @@ -29,20 +29,45 @@ const bestOf = (obj: any, keys: string[]) => {
}
}

const expandSpliceAi = ref(false)
const expandMMSplice = ref(false)

const SpliceAiKeys = [
'SpliceAI-acc-gain',
'SpliceAi-acc-loss',
'SpliceAi-don-gain',
'SpliceAi-don-loss'
]
const MMSpliceKeys = [
'MMSp_acceptorIntron',
'MMSp_acceptor',
'MMSp_exon',
'MMSp_donor',
'MMSp_donorIntron'
]

const bestSpliceAi = computed(() => {
const keys = ['SpliceAI-acc-gain', 'SpliceAi-acc-loss', 'SpliceAi-don-gain', 'SpliceAi-don-loss']
return bestOf(props.varAnnos?.cadd, keys)
return bestOf(props.varAnnos?.cadd, SpliceAiKeys)
})

const allSpliceAi = computed(() => {
const res: any = {}
for (const key of SpliceAiKeys) {
res[key] = props.varAnnos?.cadd[key]
}
return res
})

const bestMMSplice = computed(() => {
const keys = [
'MMSp_acceptorIntron',
'MMSp_acceptor',
'MMSp_exon',
'MMSp_donor',
'MMSp_donorIntron'
]
return bestOf(props.varAnnos?.cadd, keys)
return bestOf(props.varAnnos?.cadd, MMSpliceKeys)
})

const allMMSplice = computed(() => {
const res: any = {}
for (const key of MMSpliceKeys) {
res[key] = props.varAnnos?.cadd[key]
}
return res
})

const decodeMultiDbnsfp = (s: string): number | null => {
Expand Down Expand Up @@ -333,7 +358,22 @@ const polyphenScore = computed((): number | null =>
</tr>

<tr>
<th class="align-middle">MMSplice</th>
<th class="align-middle">
MMSplice
<!-- Toggle Button -->
<v-btn
variant="outlined"
size="30"
color=""
icon
:disabled="!bestMMSplice.key || bestMMSplice.score === Infinity"
@click="expandMMSplice = !expandMMSplice"
>
<v-icon>
{{ expandMMSplice ? 'mdi-chevron-down' : 'mdi-chevron-right' }}
</v-icon>
</v-btn>
</th>
<template v-if="bestMMSplice.key && bestMMSplice.score !== Infinity">
<td class="text-center align-middle">
{{ bestMMSplice.score }}
Expand All @@ -355,6 +395,23 @@ const polyphenScore = computed((): number | null =>
</td>
</tr>

<template v-if="expandMMSplice">
<tr v-for="(score, index) in allMMSplice" :key="index">
<th class="text-center align-middle">{{ index }}</th>
<td>{{ score }}</td>
<td class="text-center align-middle">
<ScoreDisplay
:range-lower="0"
:range-upper="1"
:height="12"
font-size="10px"
:value="score"
/>
</td>
<td class="text-center align-middle">&mdash;</td>
</tr>
</template>

<tr>
<th class="align-middle">MPC</th>
<template v-if="mpcScore && mpcScore !== Infinity">
Expand Down Expand Up @@ -605,7 +662,22 @@ const polyphenScore = computed((): number | null =>
</tr>

<tr>
<th class="align-middle">SpliceAI</th>
<th class="align-middle">
SpliceAI
<!-- Toggle Button -->
<v-btn
variant="outlined"
size="30"
color=""
icon
:disabled="!bestSpliceAi.key || bestSpliceAi.score === Infinity"
@click="expandSpliceAi = !expandSpliceAi"
>
<v-icon>
{{ expandSpliceAi ? 'mdi-chevron-down' : 'mdi-chevron-right' }}
</v-icon>
</v-btn>
</th>
<template v-if="bestSpliceAi.key && bestSpliceAi.score !== Infinity">
<td class="text-center align-middle">
{{ bestSpliceAi.score }}
Expand All @@ -627,6 +699,23 @@ const polyphenScore = computed((): number | null =>
</td>
</tr>

<template v-if="expandSpliceAi">
<tr v-for="(score, index) in allSpliceAi" :key="index">
<th class="text-center align-middle">{{ index }}</th>
<td>{{ score }}</td>
<td class="text-center align-middle">
<ScoreDisplay
:range-lower="0"
:range-upper="1"
:height="12"
font-size="10px"
:value="score"
/>
</td>
<td class="text-center align-middle">&mdash;</td>
</tr>
</template>

<tr>
<th class="align-middle">REVEL</th>
<template v-if="revelScore && revelScore !== Infinity">
Expand Down
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