m

index.js

@@ -20,7 +20,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.findDistance = exports.getInteractionsFromEntry = exports.getEntryFromGeneName = exports.getEnrty = exports.readOffset = exports.makeIndex = void 0;
+exports.getInteractionsFromEntry = exports.getEntryFromGeneName = exports.getEnrty = exports.readOffset = exports.makeIndex = void 0;
 const fs_1 = __importDefault(require("fs"));
 const readline_1 = __importDefault(require("readline"));
 const fast_xml_parser_1 = require("fast-xml-parser");
@@ -169,23 +169,3 @@ const getInteractionsFromEntry = (json) => __awaiter(void 0, void 0, void 0, fun
     return res;
 });
 exports.getInteractionsFromEntry = getInteractionsFromEntry;
-const findDistance = (idmappingPath, dbPath, geneNameA, geneNameB, maxDistance = 6) => __awaiter(void 0, void 0, void 0, function* () {
-    let rounds = [[geneNameA]];
-    let run = true;
-    let nIter = 0;
-    while (nIter <= maxDistance && run) {
-        for (const gA of rounds[nIter]) {
-            console.log(nIter, gA);
-            const tmp = yield getInteractionsFromEntry(yield getEntryFromGeneName(idmappingPath, dbPath, gA));
-            if (tmp.includes(geneNameB)) {
-                run = false;
-                break;
-            }
-            rounds.push(tmp);
-        }
-        nIter++;
-    }
-    //console.log(rounds);
-    return nIter;
-});
-exports.findDistance = findDistance;

test.js

@@ -9,7 +9,6 @@ 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
@@ -19,7 +18,5 @@ const _1 = require(".");
     // 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 dist = yield (0, _1.findDistance)(idmappingPath, uniprotDB, 'TTC23L', 'HOOK2');
-    console.log('dist', dist);
+    // console.log(tmp);    
 }))();

test.ts

@@ -1,4 +1,4 @@
-import { makeIndex, readOffset, getEnrty, getEntryFromGeneName, getInteractionsFromEntry,findDistance } from ".";
+import { makeIndex, readOffset, getEnrty, getEntryFromGeneName, getInteractionsFromEntry } from ".";
 import fs from 'fs'
 import jsonata from 'jsonata'
 (async()=>{
@@ -12,10 +12,5 @@ import jsonata from 'jsonata'
     // console.log(await getInteractionsFromEntry(n))
 
     // const tmp = await getInteractionsFromEntry(await getEntryFromGeneName(idmappingPath, uniprotDB, 'UBQLN1'))
-    // console.log(tmp);
-    
-    const dist = await findDistance(idmappingPath, uniprotDB, 'TTC23L','HSPA8')
-    console.log('dist',dist);
-    
-    
+    // console.log(tmp);    
 })()