chore: take gene-peaks file as stdin to allow custom files

docs/setting_up_a_node.md

@@ -187,7 +187,7 @@ docker compose up -d
 First, import the assembly gene list and gene-peak association data into the database using the following command:
 
 ```bash
-docker compose exec epivar-server node ./scripts/import-genes.mjs
+docker compose exec -i epivar-server node ./scripts/import-genes.mjs < ./input-files/flu-infection-gene-peaks.csv
 ```
 
 Then, import peaks and pre-computed peak matrix values into the database using the following command:

readme.md

@@ -205,15 +205,12 @@ The different data sources to generate/prepare are:
 
  - **Genes:** lists of gene names mapped to their characteristics, and features 
    associated with specific genes.
-     - **Import with:** `node ./scripts/import-genes.mjs`
-     - **Input:** `./input-files/flu-infection-genes.txt` and 
+     - **Import with:** e.g., `node ./scripts/import-genes.mjs < ./input-files/flu-infection-gene-peaks.csv`
+     - **Input:** A pre-computed gene list for the assembly specified in `config.js` and a file resembling
        `./input-files/flu-infection-gene-peaks.csv` 
        - Examples for these files / the versions used for the Aracena *et al.* instance 
          of the portal are already [in the repository](./input-files).
      - **Format:**
-       - `flu-infection-genes.txt`: TSV file with *no header row*. Columns are: 
-         gene name, chromosome with `chr` prefix, start coordinate, end coordinate,
-         strand (`+` or `-`).
        - `flu-infection-gene-peaks.csv`: CSV *with header row*:
          `"symbol","peak_ids","feature_type"` where `symbol` is gene name, `peak_ids`
          is a feature string (e.g., `chr1_9998_11177`), and `feature_type` is the name

scripts/import-genes.mjs

@@ -1,16 +1,15 @@
 import fs from "node:fs";
-import path from "node:path";
-
+import process from "node:process";
 import parseCSVSync from "csv-parse/lib/sync";
 
-import envConfig from "../envConfig.js";
+import config from "../config.js";
 
-const ASSAY_NAME_RNASEQ = "RNA-seq";
+import {genePathsByAssemblyID} from "../data/assemblies/index.mjs";
 
-// TODO: should be dependent on assembly + a pre-computed list
-const genesPath = path.join(envConfig.INPUT_FILES_DIR, 'flu-infection-genes.txt');
+const ASSAY_NAME_RNASEQ = "RNA-seq";
 
-const genesFeaturesPath = path.join(envConfig.INPUT_FILES_DIR, 'flu-infection-gene-peaks.csv');
+const genesPath = genePathsByAssemblyID[config.assembly];
+const genesFeaturesPath = process.argv[2] || "/dev/stdin";
 
 import {precomputedPoints} from "./_common.mjs";