m

index.js

@@ -64,7 +64,7 @@ const readOffset = (path, from, to) => {
     return new Promise((resolve, reject) => __awaiter(void 0, void 0, void 0, function* () {
         const size = to - from;
         const buffer = Buffer.alloc(size);
-        let filehandle = null;
+        let filehandle;
         try {
             filehandle = yield fs_1.default.promises.open(path, 'r+');
             yield filehandle.read(buffer, 0, buffer.length, from);
@@ -163,9 +163,8 @@ const getInteractionsFromEntry = (json) => __awaiter(void 0, void 0, void 0, fun
             .flatMap((e) => e.match(/[A-Z][A-Z0-9]{2,}/g));
     }
     let res = [...new Set([...genes_scope_inter, ...genes_interactant, ...comment_subunits_genes])].sort().filter((e) => typeof e === 'string').filter(_ => _);
-    console.log(res);
     if (res.length > 0)
-        res = res.flatMap((e) => e.match(/[A-Z][A-Z0-9]{2,}/g)).filter(_ => _);
+        res = res.flatMap((e) => e.match(/[A-Z]{2,}[A-Z0-9]{1,}/g)).filter(_ => _);
     return res;
 });
 exports.getInteractionsFromEntry = getInteractionsFromEntry;

index.ts

@@ -36,7 +36,7 @@ const readOffset = (path: string, from:number, to:number) => {
     return new Promise<string>(async (resolve, reject) => {
         const size = to - from
         const buffer = Buffer.alloc(size);
-        let filehandle = null;
+        let filehandle
         try {
             filehandle = await fs.promises.open(path, 'r+');
             await filehandle.read(buffer, 0, buffer.length, from);
@@ -123,10 +123,8 @@ const getInteractionsFromEntry = async (json:any) => {
     }
 
     let res = [...new Set([...genes_scope_inter, ...genes_interactant, ...comment_subunits_genes])].sort().filter((e:any) => typeof e === 'string').filter(_=>_)
-
-    console.log(res);
     
-    if(res.length > 0) res = res.flatMap((e:any) => e.match(/[A-Z][A-Z0-9]{2,}/g)).filter(_=>_)
+    if(res.length > 0) res = res.flatMap((e:any) => e.match(/[A-Z]{2,}[A-Z0-9]{1,}/g)).filter(_=>_)
     
     return res
 }

test.js

@@ -9,6 +9,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
     });
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const _1 = require(".");
 (() => __awaiter(void 0, void 0, void 0, function* () {
     // https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/
     // https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz
@@ -17,6 +18,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
     // const n = await getEntryFromGeneName(idmappingPath, uniprotDB, 'TTC23L')
     // await fs.promises.writeFile('test/test-CITED2.json', JSON.stringify(n, null, 4))
     // console.log(await getInteractionsFromEntry(n))
-    // const tmp = await getInteractionsFromEntry(await getEntryFromGeneName(idmappingPath, uniprotDB, 'UBQLN1'))
-    // console.log(tmp);    
+    const tmp = yield (0, _1.getInteractionsFromEntry)(yield (0, _1.getEntryFromGeneName)(idmappingPath, uniprotDB, 'UBQLN1'));
+    console.log(tmp);
 }))();

test.ts

@@ -11,6 +11,6 @@ import jsonata from 'jsonata'
     // await fs.promises.writeFile('test/test-CITED2.json', JSON.stringify(n, null, 4))
     // console.log(await getInteractionsFromEntry(n))
 
-    // const tmp = await getInteractionsFromEntry(await getEntryFromGeneName(idmappingPath, uniprotDB, 'UBQLN1'))
-    // console.log(tmp);    
+    const tmp = await getInteractionsFromEntry(await getEntryFromGeneName(idmappingPath, uniprotDB, 'UBQLN1'))
+    console.log(tmp);    
 })()