{ "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": [ "
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sample_id
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" ], "text/plain": [ "gene_id ENSG00000278704.1 ENSG00000277400.1 \\\n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 0 \n", "\n", "gene_id ENSG00000274847.1 ENSG00000277428.1 \\\n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 0 \n", "\n", "gene_id ENSG00000276256.1 ENSG00000278198.1 \\\n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 0 \n", "\n", "gene_id ENSG00000276932.1 ENSG00000273496.1 \\\n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 0 \n", "\n", "gene_id ENSG00000273735.4 ENSG00000273517.1 \\\n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 0 \n", "\n", "gene_id ... ENSG00000237801.6_PAR_Y \\\n", "sample_id ... \n", "5b2072ee-b856-45c4-9c14-449654a40600 ... 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 ... 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 ... 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 ... 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 ... 0 \n", "\n", "gene_id ENSG00000237040.6_PAR_Y \\\n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 \n", "\n", "gene_id ENSG00000124333.15_PAR_Y \\\n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 \n", "\n", "gene_id ENSG00000228410.6_PAR_Y \\\n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 \n", "\n", "gene_id ENSG00000223484.7_PAR_Y \\\n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 \n", "\n", "gene_id ENSG00000124334.17_PAR_Y \\\n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 \n", "\n", "gene_id ENSG00000185203.12_PAR_Y \\\n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 \n", "\n", "gene_id ENSG00000270726.6_PAR_Y \\\n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 \n", "\n", "gene_id ENSG00000182484.15_PAR_Y \\\n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 \n", "\n", "gene_id ENSG00000227159.8_PAR_Y \n", "sample_id \n", "5b2072ee-b856-45c4-9c14-449654a40600 0 \n", "2ba5b847-887f-415a-a7f3-94e6ea4d3800 0 \n", "0b1cf6de-f98f-4020-baa7-c4fc518e5f00 0 \n", "bd879832-e177-4fca-b1ea-d1553518e700 0 \n", "03737fb6-a59c-4618-a4e5-5fc657e42900 0 \n", "\n", "[5 rows x 64837 columns]" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import pandas as pd\n", "FILEPATH = \"/vast/projects/deep-recount3/data/tcga.gene_sums.BRCA.G029\"\n", "df = pd.read_csv(FILEPATH, header=2, sep=\"\\t\", index_col=\"gene_id\", on_bad_lines=\"skip\")\n", "df.columns.name = \"sample_id\"\n", "df = df.transpose()\n", "# df.head()" ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [], "source": [ "from sklearn.datasets import load_svmlight_file, dump_svmlight_file\n", "import numpy as np\n", "\n", "cols = df.columns.tolist()\n", "vals = df.values\n", "dump_svmlight_file(X=vals, y=np.arange(0, vals.shape[0]), f=\"sparse_BRCA.txt\")" ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "'ENSG00000237613.2'" ] }, "execution_count": 18, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cols[6121]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Dataset Loading script" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3.10.9 ('recount')", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.10.9" }, "orig_nbformat": 4, "vscode": { "interpreter": { "hash": "ed875d186ce08f1d09fded8cb618f7757e0d4e9a9ff702057ff3018e00fc337a" } } }, "nbformat": 4, "nbformat_minor": 2 }