Load Foldseek Data on TM Align Compare Page (#237)

* Changed directory name in delete_all py script from string to os.join so it works on windows, and hopefully universally. * TM Align page now computes Foldseek data for compare protein * Changed loading text * Ruff reformat
Venom-Biochem-Lab · Apr 15, 2024 · da5ee05 · da5ee05
1 parent de56683
commit da5ee05
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Showing 29 changed files with 135 additions and 32 deletions.
diff --git a/backend/src/api/search.py b/backend/src/api/search.py
@@ -229,3 +229,42 @@ def search_venome_similar(protein_name: str):
  raise HTTPException(500, "Error getting protein descriptions")
 
  return formatted
+
+
+@router.get(
+ "/search/venome/similar/{protein_name:str}/{protein_compare:str}",
+ response_model=SimilarProtein,
+)
+def search_venome_similar_compare(protein_name: str, protein_compare: str):
+ target = stored_pdb_file_name(protein_compare)
+ # ignore the first since it's itself as the most similar
+ try:
+ similar = easy_search(
+ stored_pdb_file_name(protein_name),
+ target,
+ out_format="target,prob,evalue,qstart,qend",
+ ) # qend,qstart refer to alignment
+ formatted = [
+ SimilarProtein(
+ name=name.rstrip(".pdb"),
+ prob=prob,
+ evalue=evalue,
+ qstart=qstart,
+ qend=qend,
+ alntmscore=0,
+ )
+ for [name, prob, evalue, qstart, qend] in similar
+ ]
+ except Exception:
+ raise HTTPException(404, "Error in 'foldseek easy-search' command")
+
+ try:
+ # populate protein descriptions for the similar proteins
+ descriptions = get_descriptions([s.name for s in formatted])
+ if descriptions is not None:
+ for f, d in zip(formatted, descriptions):
+ f.description = d
+ except Exception:
+ raise HTTPException(500, "Error getting protein descriptions")
+
+ return formatted[0]
diff --git a/backend/src/data/pdbAlphaFold/.gitignore b/backend/src/data/pdbAlphaFold/.gitignore
@@ -1 +1 @@
-*.pdb
+*.pdb 
diff --git a/frontend/src/lib/openapi/core/ApiError.ts b/frontend/src/lib/openapi/core/ApiError.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/core/ApiRequestOptions.ts b/frontend/src/lib/openapi/core/ApiRequestOptions.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/core/ApiResult.ts b/frontend/src/lib/openapi/core/ApiResult.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/core/CancelablePromise.ts b/frontend/src/lib/openapi/core/CancelablePromise.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
@@ -85,9 +85,9 @@ export class CancelablePromise<T> implements Promise<T> {
  });
  }
 
-  get [Symbol.toStringTag]() {
-  return "Cancellable Promise";
-  }
+ get [Symbol.toStringTag]() {
+ return "Cancellable Promise";
+ }
 
  public then<TResult1 = T, TResult2 = never>(
  onFulfilled?: ((value: T) => TResult1 | PromiseLike<TResult1>) | null,

diff --git a/frontend/src/lib/openapi/core/OpenAPI.ts b/frontend/src/lib/openapi/core/OpenAPI.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/core/request.ts b/frontend/src/lib/openapi/core/request.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
@@ -164,7 +164,7 @@ export const getHeaders = async (config: OpenAPIConfig, options: ApiRequestOptio
  headers['Authorization'] = `Basic ${credentials}`;
  }
 
- if (options.body) {
+ if (options.body !== undefined) {
  if (options.mediaType) {
  headers['Content-Type'] = options.mediaType;
  } else if (isBlob(options.body)) {

diff --git a/frontend/src/lib/openapi/index.ts b/frontend/src/lib/openapi/index.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/EditBody.ts b/frontend/src/lib/openapi/models/EditBody.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/HTTPValidationError.ts b/frontend/src/lib/openapi/models/HTTPValidationError.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/LoginBody.ts b/frontend/src/lib/openapi/models/LoginBody.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/LoginResponse.ts b/frontend/src/lib/openapi/models/LoginResponse.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/ProteinEditSuccess.ts b/frontend/src/lib/openapi/models/ProteinEditSuccess.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/ProteinEntry.ts b/frontend/src/lib/openapi/models/ProteinEntry.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/RangeFilter.ts b/frontend/src/lib/openapi/models/RangeFilter.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/SearchProteinsBody.ts b/frontend/src/lib/openapi/models/SearchProteinsBody.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/SearchProteinsResults.ts b/frontend/src/lib/openapi/models/SearchProteinsResults.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/SimilarProtein.ts b/frontend/src/lib/openapi/models/SimilarProtein.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/Tutorial.ts b/frontend/src/lib/openapi/models/Tutorial.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/TutorialEdit.ts b/frontend/src/lib/openapi/models/TutorialEdit.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/TutorialUpload.ts b/frontend/src/lib/openapi/models/TutorialUpload.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/UploadBody.ts b/frontend/src/lib/openapi/models/UploadBody.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/UploadError.ts b/frontend/src/lib/openapi/models/UploadError.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/UploadPNGBody.ts b/frontend/src/lib/openapi/models/UploadPNGBody.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/models/ValidationError.ts b/frontend/src/lib/openapi/models/ValidationError.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */

diff --git a/frontend/src/lib/openapi/services/DefaultService.ts b/frontend/src/lib/openapi/services/DefaultService.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
@@ -112,6 +112,29 @@ export class DefaultService {
  },
  });
  }
+ /**
+ * Search Venome Similar Compare
+ * @param proteinName
+ * @param proteinCompare
+ * @returns SimilarProtein Successful Response
+ * @throws ApiError
+ */
+ public static searchVenomeSimilarCompare(
+ proteinName: string,
+ proteinCompare: string,
+ ): CancelablePromise<SimilarProtein> {
+ return __request(OpenAPI, {
+ method: 'GET',
+ url: '/search/venome/similar/{protein_name}/{protein_compare}',
+ path: {
+ 'protein_name': proteinName,
+ 'protein_compare': proteinCompare,
+ },
+ errors: {
+ 422: `Validation Error`,
+ },
+ });
+ }
  /**
  * Get Pdb File
  * @param proteinName

diff --git a/frontend/src/routes/Align.svelte b/frontend/src/routes/Align.svelte
@@ -2,19 +2,22 @@
  import TMAlignEntry from "./TMAlignEntry.svelte";
 
  import { onMount } from "svelte";
- import { Backend, BACKEND_URL, type ProteinEntry } from "../lib/backend";
+ import { Backend, BACKEND_URL, type SimilarProtein, type ProteinEntry } from "../lib/backend";
  import Molstar from "../lib/Molstar.svelte";
  import DelayedSpinner from "../lib/DelayedSpinner.svelte";
  import { DownloadOutline } from "flowbite-svelte-icons";
  import { Button } from "flowbite-svelte";
  import * as d3 from "d3";
  import { undoFormatProteinName } from "../lib/format";
+ import AlignBlock from "../lib/AlignBlock.svelte";
 
  export let proteinA: string;
  export let proteinB: string;
  let combined = proteinA + "/" + proteinB;
  let entryA: ProteinEntry | null = null;
  let entryB: ProteinEntry | null = null;
+ let foldseekData: SimilarProtein;
+ let foldseekError = false;
  let error = false;
 
  const dark2green = d3.schemeDark2[0];
@@ -34,6 +37,17 @@
  entryA = await Backend.getProteinEntry(proteinA);
  entryB = await Backend.getProteinEntry(proteinB);
 
+ try {
+ foldseekData = await Backend.searchVenomeSimilarCompare(proteinA, proteinB)
+ } catch (e) {
+ console.error(e);
+ console.error(
+ "NEED TO DOWNLOAD FOLDSEEK IN THE SERVER. SEE THE SERVER ERROR MESSAGE."
+ );
+ foldseekError = true;
+ }
+ 
+
  // if we could not find the entry, the id is garbo
  if (entryA == null || entryB == null) error = true;
  console.log(entryA, entryB);
@@ -58,6 +72,33 @@
  </div>
  <TMAlignEntry entry={entryA} color={dark2green} />
  <TMAlignEntry entry={entryB} color={dark2orange} />
+ <h1>
+ Foldseek Data
+ </h1>
+ {#if foldseekData === undefined && !foldseekError}
+ <DelayedSpinner
+ text="Loading Foldseek..."
+ textRight
+ msDelay={0}
+ />
+ {:else if foldseekData !== undefined}
+ <div>
+ <b>Prob. Match:</b> {foldseekData.prob}
+ </div>
+ <div>
+ <b>E-Value:</b> {foldseekData.evalue}
+ </div>
+ <div>
+ <b>Region of Similarity</b>
+ <AlignBlock
+ width={260}
+ height={20}
+ ogLength={entryA.length}
+ qstart={foldseekData.qstart}
+ qend={foldseekData.qend}
+ />
+ </div>
+ {/if}
  <div style="width: 300px;" class="mt-3">
  <Button href="{BACKEND_URL}/protein/pdb/{combined}"
  >Download Aligned PDB File<DownloadOutline

diff --git a/galaxy/delete_all.py b/galaxy/delete_all.py
@@ -1,7 +1,7 @@
 import requests
 import os
 
-DIR = "../backend/src/data/pdbAlphaFold"
+DIR = os.path.join('..', 'backend', 'src', 'data', 'pdbAlphaFold')
 
 
 def delete_protein_files():