From b6049948853d5e0da47e295c367025908c4a7623 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Thu, 25 Apr 2024 18:03:16 +0200
Subject: [PATCH] handle case when seperator in gene_name is _ instead of __
---
components/content/ArticleStructure.vue | 14 ++++++++--
components/content/PdockqMatrix.vue | 28 +++++++++++++-------
components/content/StructureDb.vue | 13 +++++++--
components/content/SystemOperonStructure.vue | 20 +++++++++-----
4 files changed, 55 insertions(+), 20 deletions(-)
diff --git a/components/content/ArticleStructure.vue b/components/content/ArticleStructure.vue
index 814b1da0..85e97f86 100644
--- a/components/content/ArticleStructure.vue
+++ b/components/content/ArticleStructure.vue
@@ -45,11 +45,21 @@ onMounted(() => {
fetchStructures()
})
+function extractGeneName(name: string) {
+ if (name.includes("__")) {
+ return name.split("__")[1]
+ }
+ if (name.includes("_")) {
+ return name.split("_")[1]
+ }
+ return undefined
+}
+
function namesToCollapsibleChips(names: string[], systemDir: string, file: string | null = null) {
if (file === null) {
- return names.filter((it) => it !== "").map(it => ({ title: it.split("__")[1] }))
+ return names.filter((it) => it !== "").map(it => ({ title: extractGeneName(it) }))
} else {
- return names.filter((it) => it !== "").map(it => ({ title: it.split("__")[1], href: `/wiki/${systemDir}/${file}` }))
+ return names.filter((it) => it !== "").map(it => ({ title: extractGeneName(it), href: `/wiki/${systemDir}/${file}` }))
}
}
function pdbNameToCif(pdbPath: string) {
diff --git a/components/content/PdockqMatrix.vue b/components/content/PdockqMatrix.vue
index f39b4ffc..aa22e4f0 100644
--- a/components/content/PdockqMatrix.vue
+++ b/components/content/PdockqMatrix.vue
@@ -65,22 +65,30 @@ const computedSystem = computed(() => {
return toValPage?.system ?? toValPage?.title ?? undefined
})
-
+function extractGeneName(name: string) {
+ if (name.includes("__")) {
+ return name.split("__")[1]
+ }
+ if (name.includes("_")) {
+ return name.split("_")[1]
+ }
+ return undefined
+}
const groupedPdocks = computed(() => {
const toValData = toValue(data)
- const getSeqName = (d) => {
- if (d.includes("__")) {
- return d.split("__")[1]
- } else {
- return d
- }
- }
+ // const getSeqName = (d) => {
+ // if (d.includes("__")) {
+ // return d.split("__")[1]
+ // } else {
+ // return d
+ // }
+ // }
if (toValData?.hits) {
return d3.groups(toValData.hits.flatMap(({ system, pDockQ, pdb, nb_sys, proteins_in_the_prediction, system_genes }) => {
if (proteins_in_the_prediction.length === 2) {
- const sanitizedSystemGenes = system_genes.map(getSeqName)
- const sanitizedProteins = proteins_in_the_prediction.map(getSeqName)
+ const sanitizedSystemGenes = system_genes.map(extractGeneName)
+ const sanitizedProteins = proteins_in_the_prediction.map(extractGeneName)
const setProteins = new Set(sanitizedProteins)
const key = system_genes.sort().join(" / ")
if (setProteins.size === 2) {
diff --git a/components/content/StructureDb.vue b/components/content/StructureDb.vue
index 5af72db9..417a7e70 100644
--- a/components/content/StructureDb.vue
+++ b/components/content/StructureDb.vue
@@ -137,12 +137,21 @@ function toFolseekUrl(item: Item) {
return toValue(refinedUrl)
}
+function extractGeneName(name: string) {
+ if (name.includes("__")) {
+ return name.split("__")[1]
+ }
+ if (name.includes("_")) {
+ return name.split("_")[1]
+ }
+ return undefined
+}
function namesToCollapsibleChips(names: string[], systemDir: string, file: string | null = null) {
if (file === null) {
- return names.filter((it) => it !== "").map(it => ({ title: it.split("__")[1] }))
+ return names.filter((it) => it !== "").map(it => ({ title: extractGeneName(it) }))
} else {
- return names.filter((it) => it !== "").map(it => ({ title: it.split("__")[1], href: `/wiki/${systemDir}/${file}` }))
+ return names.filter((it) => it !== "").map(it => ({ title: extractGeneName(it), href: `/wiki/${systemDir}/${file}` }))
}
}
diff --git a/components/content/SystemOperonStructure.vue b/components/content/SystemOperonStructure.vue
index 379be425..1a149736 100644
--- a/components/content/SystemOperonStructure.vue
+++ b/components/content/SystemOperonStructure.vue
@@ -34,29 +34,37 @@ const monomerStructures = computed(() => {
structImg: `${struct.pdb.split(".pdb")[0]}.png`,
structPath: struct.pdb,
proteins_in_the_prediction: struct.proteins_in_the_prediction.map(prot => {
- return prot.split("__")[1]
+ return extractGeneName(prot)
})
}
})
}
})
+
+function extractGeneName(name: string) {
+ if (name.includes("__")) {
+ return name.split("__")[1]
+ }
+ if (name.includes("_")) {
+ return name.split("_")[1]
+ }
+ return undefined
+}
+
const sanitizedHits = computed<StructureOperonGeneWithImg[]>(() => {
const toValMsResponse = toValue(msResponse)
if (toValMsResponse && toValMsResponse?.hits?.length > 0) {
return toValMsResponse.hits.map(hit => {
// get structure information for this prot
const monomerStructuresVal = toValue(monomerStructures)
- const sanitizedGene = hit.gene.split("__")[1]
- const sanitizedExangeableGenes = hit.exchangeables.map(g => g.split("__")[1])
+ const sanitizedGene = extractGeneName(hit.gene)
+ const sanitizedExangeableGenes = hit.exchangeables.map(extractGeneName)
const genesAndSynonymous = new Set([sanitizedGene, ...sanitizedExangeableGenes])
if (monomerStructuresVal) {
const struct = monomerStructuresVal.find((struct) => {
return genesAndSynonymous.has(struct.proteins_in_the_prediction[0])
})
- if (struct === undefined) {
- console.log(hit)
- }
const rawImgUrl = joinURL(`/${system.toLowerCase()}`, struct?.structImg ?? '')
const rawStructUrl = joinURL(`/${system.toLowerCase()}`, struct?.structPath ?? '')
const { refinedUrl: structImgHref } = useRefinedUrl(rawImgUrl)
--
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