{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Simple csv loader pipeline" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "from typing import Dict\n", "import datasets\n", "from datasets import load_from_disk\n", "import os\n", "import json\n", "import s3fs\n", "from huggingface_hub import hf_hub_download\n", "\n", "s3 = s3fs.S3FileSystem(anon=True)" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "\n", " \n", " # def url_list(\n", " # tcga_dataset_ids: List[str],\n", " # gtex_dataset_ids: List[str],\n", " # sra_dataset_ids: List[str],\n", " # ):\n", " " ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "# recount = Recount3Index()\n", "\n", "# recount.public_dataset_url(subset=\"tcga\", dataset_id=\"BRCA\")" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
gene_id | \n", "ENSG00000278704.1 | \n", "ENSG00000277400.1 | \n", "ENSG00000274847.1 | \n", "ENSG00000277428.1 | \n", "ENSG00000276256.1 | \n", "ENSG00000278198.1 | \n", "ENSG00000276932.1 | \n", "ENSG00000273496.1 | \n", "ENSG00000273735.4 | \n", "ENSG00000273517.1 | \n", "... | \n", "ENSG00000237801.6_PAR_Y | \n", "ENSG00000237040.6_PAR_Y | \n", "ENSG00000124333.15_PAR_Y | \n", "ENSG00000228410.6_PAR_Y | \n", "ENSG00000223484.7_PAR_Y | \n", "ENSG00000124334.17_PAR_Y | \n", "ENSG00000185203.12_PAR_Y | \n", "ENSG00000270726.6_PAR_Y | \n", "ENSG00000182484.15_PAR_Y | \n", "ENSG00000227159.8_PAR_Y | \n", "
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