{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/saketkc/pysradb/blob/develop/notebooks/03.ParallelDownload.ipynb)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Parallel Download\n", "\n", "This notebook demonstrates how to download multiple SRA datasets in parallel using joblib." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# Install pysradb if not already installed\n", "try:\n", " import pysradb\n", "\n", " print(f\"pysradb {pysradb.__version__} is already installed\")\n", "except ImportError:\n", " print(\"Installing pysradb from GitHub...\")\n", " import sys\n", "\n", " !{sys.executable} -m pip install -q git+https://github.com/saketkc/pysradb\n", " print(\"pysradb installed successfully!\")" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 664 }, "colab_type": "code", "id": "kdFGQ6S9OEeP", "outputId": "7b4ba253-c30a-43ce-b96a-6ff22b887f5a" }, "outputs": [], "source": [ "# pip install git+https://github.com/saketkc/pysradb" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 34 }, "colab_type": "code", "id": "fGSXNG8LOLDI", "outputId": "4d53c90e-589f-43af-a1ad-e6d6cea9d9c7" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Requirement already satisfied: joblib in /home/saket/miniforge3/lib/python3.12/site-packages (1.5.2)\n", "Note: you may need to restart the kernel to use updated packages.\n" ] } ], "source": [ "pip install joblib" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "colab": {}, "colab_type": "code", "id": "CiEBTC4IO-pn" }, "outputs": [], "source": [ "from joblib import Parallel, delayed" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "colab": {}, "colab_type": "code", "id": "6vD2huxFOMZ_" }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/saket/miniforge3/lib/python3.12/site-packages/pysradb/utils.py:14: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n", " from tqdm.autonotebook import tqdm\n" ] } ], "source": [ "from pysradb.sraweb import SRAweb\n", "\n", "db = SRAweb()" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 1000 }, "colab_type": "code", "id": "7jm1NDReOSgP", "outputId": "05ec84ac-f723-4235-a32b-5eaec0ed8462" }, "outputs": [ { "data": { "text/html": [ "
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run_accessionstudy_accessionstudy_titleexperiment_accessionexperiment_titleexperiment_descorganism_taxidorganism_namelibrary_namelibrary_strategy...source_namecell linetreatment timelibrary typeena_fastq_httpena_fastq_http_1ena_fastq_http_2ena_fastq_ftpena_fastq_ftp_1ena_fastq_ftp_2
0SRR5227288SRP098789Selective stalling of human translation throug...SRX2536403GSM2475997: 1.5 µM PF-067446846, 10 min, rep 1...GSM2475997: 1.5 µM PF-067446846, 10 min, rep 1...9606Homo sapiens<NA>OTHER...Huh7_1.5 µM PF-067446846_10 min_ribo-seqHuh710 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
1SRR5227289SRP098789Selective stalling of human translation throug...SRX2536404GSM2475998: 1.5 µM PF-067446846, 10 min, rep 2...GSM2475998: 1.5 µM PF-067446846, 10 min, rep 2...9606Homo sapiens<NA>OTHER...Huh7_1.5 µM PF-067446846_10 min_ribo-seqHuh710 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
2SRR5227290SRP098789Selective stalling of human translation throug...SRX2536405GSM2475999: 1.5 µM PF-067446846, 10 min, rep 3...GSM2475999: 1.5 µM PF-067446846, 10 min, rep 3...9606Homo sapiens<NA>OTHER...Huh7_1.5 µM PF-067446846_10 min_ribo-seqHuh710 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
3SRR5227291SRP098789Selective stalling of human translation throug...SRX2536406GSM2476000: 0.3 µM PF-067446846, 10 min, rep 1...GSM2476000: 0.3 µM PF-067446846, 10 min, rep 1...9606Homo sapiens<NA>OTHER...Huh7_0.3 µM PF-067446846_10 min_ribo-seqHuh710 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
4SRR5227292SRP098789Selective stalling of human translation throug...SRX2536407GSM2476001: 0.3 µM PF-067446846, 10 min, rep 2...GSM2476001: 0.3 µM PF-067446846, 10 min, rep 2...9606Homo sapiens<NA>OTHER...Huh7_0.3 µM PF-067446846_10 min_ribo-seqHuh710 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
5SRR5227293SRP098789Selective stalling of human translation throug...SRX2536408GSM2476002: 0.3 µM PF-067446846, 10 min, rep 3...GSM2476002: 0.3 µM PF-067446846, 10 min, rep 3...9606Homo sapiens<NA>OTHER...Huh7_0.3 µM PF-067446846_10 min_ribo-seqHuh710 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
6SRR5227294SRP098789Selective stalling of human translation throug...SRX2536409GSM2476003: vehicle, 10 min rep 1; Homo sapien...GSM2476003: vehicle, 10 min rep 1; Homo sapien...9606Homo sapiens<NA>OTHER...Huh7_vehicle_10 min_ribo-seqHuh710 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/004...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
7SRR5227295SRP098789Selective stalling of human translation throug...SRX2536410GSM2476004: vehicle, 10 min rep 2; Homo sapien...GSM2476004: vehicle, 10 min rep 2; Homo sapien...9606Homo sapiens<NA>OTHER...Huh7_vehicle_10 min_ribo-seqHuh710 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/005...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
8SRR5227296SRP098789Selective stalling of human translation throug...SRX2536411GSM2476005: vehicle, 10 min rep 3; Homo sapien...GSM2476005: vehicle, 10 min rep 3; Homo sapien...9606Homo sapiens<NA>OTHER...Huh7_vehicle_10 min_ribo-seqHuh710 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/006...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
9SRR5227297SRP098789Selective stalling of human translation throug...SRX2536412GSM2476006: 1.5 µM PF-067446846, 60 min, rep 1...GSM2476006: 1.5 µM PF-067446846, 60 min, rep 1...9606Homo sapiens<NA>OTHER...Huh7_1.5 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/007...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
10SRR5227298SRP098789Selective stalling of human translation throug...SRX2536413GSM2476007: 1.5 µM PF-067446846, 60 min, rep 2...GSM2476007: 1.5 µM PF-067446846, 60 min, rep 2...9606Homo sapiens<NA>OTHER...Huh7_1.5 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
11SRR5227299SRP098789Selective stalling of human translation throug...SRX2536414GSM2476008: 1.5 µM PF-067446846, 60 min, rep 3...GSM2476008: 1.5 µM PF-067446846, 60 min, rep 3...9606Homo sapiens<NA>OTHER...Huh7_1.5 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
12SRR5227300SRP098789Selective stalling of human translation throug...SRX2536415GSM2476009: 0.3 µM PF-067446846, 60 min, rep 1...GSM2476009: 0.3 µM PF-067446846, 60 min, rep 1...9606Homo sapiens<NA>OTHER...Huh7_0.3 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
13SRR5227301SRP098789Selective stalling of human translation throug...SRX2536416GSM2476010: 0.3 µM PF-067446846, 60 min, rep 2...GSM2476010: 0.3 µM PF-067446846, 60 min, rep 2...9606Homo sapiens<NA>OTHER...Huh7_0.3 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
14SRR5227302SRP098789Selective stalling of human translation throug...SRX2536417GSM2476011: 0.3 µM PF-067446846, 60 min, rep 3...GSM2476011: 0.3 µM PF-067446846, 60 min, rep 3...9606Homo sapiens<NA>OTHER...Huh7_0.3 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
15SRR5227303SRP098789Selective stalling of human translation throug...SRX2536418GSM2476012: vehicle, 60 min rep 1; Homo sapien...GSM2476012: vehicle, 60 min rep 1; Homo sapien...9606Homo sapiens<NA>OTHER...Huh7_vehicle_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
16SRR5227304SRP098789Selective stalling of human translation throug...SRX2536419GSM2476013: vehicle, 60 min rep 2; Homo sapien...GSM2476013: vehicle, 60 min rep 2; Homo sapien...9606Homo sapiens<NA>OTHER...Huh7_vehicle_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/004...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
17SRR5227305SRP098789Selective stalling of human translation throug...SRX2536420GSM2476014: vehicle, 60 min rep 3; Homo sapien...GSM2476014: vehicle, 60 min rep 3; Homo sapien...9606Homo sapiens<NA>OTHER...Huh7_vehicle_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/005...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
18SRR5227306SRP098789Selective stalling of human translation throug...SRX2536421GSM2476015: 1.5 µM PF-067446846, 60 min, rep 4...GSM2476015: 1.5 µM PF-067446846, 60 min, rep 4...9606Homo sapiens<NA>OTHER...Huh7_1.5 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/006...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
19SRR5227307SRP098789Selective stalling of human translation throug...SRX2536422GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; H...GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; H...9606Homo sapiens<NA>RNA-Seq...Huh7_Veh_60 min_Ribo-seqHuh760 minRibo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/007...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
20SRR5227308SRP098789Selective stalling of human translation throug...SRX2536423GSM2476017: 1.5 µM PF-067446846, 60 min, rep 5...GSM2476017: 1.5 µM PF-067446846, 60 min, rep 5...9606Homo sapiens<NA>OTHER...Huh7_1.5 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
21SRR5227309SRP098789Selective stalling of human translation throug...SRX2536424GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; H...GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; H...9606Homo sapiens<NA>RNA-Seq...Huh7_vehcile_60 min_Ribo-seqHuh760 minRibo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
22SRR5227310SRP098789Selective stalling of human translation throug...SRX2536425GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-s...GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-s...9606Homo sapiens<NA>OTHER...Huh7_PF-06446846_60 min_mRNA-seqHuh760 minmRNA-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
23SRR5227311SRP098789Selective stalling of human translation throug...SRX2536426GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Ho...GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Ho...9606Homo sapiens<NA>RNA-Seq...Huh7_vehicle_60 min_RNA-seqHuh760 minpolyA-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
24SRR5227312SRP098789Selective stalling of human translation throug...SRX2536427GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-s...GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-s...9606Homo sapiens<NA>OTHER...Huh7_PF-06446846_60 min_mRNA-seqHuh760 minmRNA-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
25SRR5227313SRP098789Selective stalling of human translation throug...SRX2536428GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Ho...GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Ho...9606Homo sapiens<NA>RNA-Seq...Huh7_vehicle_60 min_RNA-seqHuh760 minpolyA-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
\n", "

26 rows × 54 columns

\n", "
" ], "text/plain": [ " run_accession study_accession \\\n", "0 SRR5227288 SRP098789 \n", "1 SRR5227289 SRP098789 \n", "2 SRR5227290 SRP098789 \n", "3 SRR5227291 SRP098789 \n", "4 SRR5227292 SRP098789 \n", "5 SRR5227293 SRP098789 \n", "6 SRR5227294 SRP098789 \n", "7 SRR5227295 SRP098789 \n", "8 SRR5227296 SRP098789 \n", "9 SRR5227297 SRP098789 \n", "10 SRR5227298 SRP098789 \n", "11 SRR5227299 SRP098789 \n", "12 SRR5227300 SRP098789 \n", "13 SRR5227301 SRP098789 \n", "14 SRR5227302 SRP098789 \n", "15 SRR5227303 SRP098789 \n", "16 SRR5227304 SRP098789 \n", "17 SRR5227305 SRP098789 \n", "18 SRR5227306 SRP098789 \n", "19 SRR5227307 SRP098789 \n", "20 SRR5227308 SRP098789 \n", "21 SRR5227309 SRP098789 \n", "22 SRR5227310 SRP098789 \n", "23 SRR5227311 SRP098789 \n", "24 SRR5227312 SRP098789 \n", "25 SRR5227313 SRP098789 \n", "\n", " study_title experiment_accession \\\n", "0 Selective stalling of human translation throug... SRX2536403 \n", "1 Selective stalling of human translation throug... SRX2536404 \n", "2 Selective stalling of human translation throug... SRX2536405 \n", "3 Selective stalling of human translation throug... SRX2536406 \n", "4 Selective stalling of human translation throug... SRX2536407 \n", "5 Selective stalling of human translation throug... SRX2536408 \n", "6 Selective stalling of human translation throug... SRX2536409 \n", "7 Selective stalling of human translation throug... SRX2536410 \n", "8 Selective stalling of human translation throug... SRX2536411 \n", "9 Selective stalling of human translation throug... SRX2536412 \n", "10 Selective stalling of human translation throug... SRX2536413 \n", "11 Selective stalling of human translation throug... SRX2536414 \n", "12 Selective stalling of human translation throug... SRX2536415 \n", "13 Selective stalling of human translation throug... SRX2536416 \n", "14 Selective stalling of human translation throug... SRX2536417 \n", "15 Selective stalling of human translation throug... SRX2536418 \n", "16 Selective stalling of human translation throug... SRX2536419 \n", "17 Selective stalling of human translation throug... SRX2536420 \n", "18 Selective stalling of human translation throug... SRX2536421 \n", "19 Selective stalling of human translation throug... SRX2536422 \n", "20 Selective stalling of human translation throug... SRX2536423 \n", "21 Selective stalling of human translation throug... SRX2536424 \n", "22 Selective stalling of human translation throug... SRX2536425 \n", "23 Selective stalling of human translation throug... SRX2536426 \n", "24 Selective stalling of human translation throug... SRX2536427 \n", "25 Selective stalling of human translation throug... SRX2536428 \n", "\n", " experiment_title \\\n", "0 GSM2475997: 1.5 µM PF-067446846, 10 min, rep 1... \n", "1 GSM2475998: 1.5 µM PF-067446846, 10 min, rep 2... \n", "2 GSM2475999: 1.5 µM PF-067446846, 10 min, rep 3... \n", "3 GSM2476000: 0.3 µM PF-067446846, 10 min, rep 1... \n", "4 GSM2476001: 0.3 µM PF-067446846, 10 min, rep 2... \n", "5 GSM2476002: 0.3 µM PF-067446846, 10 min, rep 3... \n", "6 GSM2476003: vehicle, 10 min rep 1; Homo sapien... \n", "7 GSM2476004: vehicle, 10 min rep 2; Homo sapien... \n", "8 GSM2476005: vehicle, 10 min rep 3; Homo sapien... \n", "9 GSM2476006: 1.5 µM PF-067446846, 60 min, rep 1... \n", "10 GSM2476007: 1.5 µM PF-067446846, 60 min, rep 2... \n", "11 GSM2476008: 1.5 µM PF-067446846, 60 min, rep 3... \n", "12 GSM2476009: 0.3 µM PF-067446846, 60 min, rep 1... \n", "13 GSM2476010: 0.3 µM PF-067446846, 60 min, rep 2... \n", "14 GSM2476011: 0.3 µM PF-067446846, 60 min, rep 3... \n", "15 GSM2476012: vehicle, 60 min rep 1; Homo sapien... \n", "16 GSM2476013: vehicle, 60 min rep 2; Homo sapien... \n", "17 GSM2476014: vehicle, 60 min rep 3; Homo sapien... \n", "18 GSM2476015: 1.5 µM PF-067446846, 60 min, rep 4... \n", "19 GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; H... \n", "20 GSM2476017: 1.5 µM PF-067446846, 60 min, rep 5... \n", "21 GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; H... \n", "22 GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-s... \n", "23 GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Ho... \n", "24 GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-s... \n", "25 GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Ho... \n", "\n", " experiment_desc organism_taxid \\\n", "0 GSM2475997: 1.5 µM PF-067446846, 10 min, rep 1... 9606 \n", "1 GSM2475998: 1.5 µM PF-067446846, 10 min, rep 2... 9606 \n", "2 GSM2475999: 1.5 µM PF-067446846, 10 min, rep 3... 9606 \n", "3 GSM2476000: 0.3 µM PF-067446846, 10 min, rep 1... 9606 \n", "4 GSM2476001: 0.3 µM PF-067446846, 10 min, rep 2... 9606 \n", "5 GSM2476002: 0.3 µM PF-067446846, 10 min, rep 3... 9606 \n", "6 GSM2476003: vehicle, 10 min rep 1; Homo sapien... 9606 \n", "7 GSM2476004: vehicle, 10 min rep 2; Homo sapien... 9606 \n", "8 GSM2476005: vehicle, 10 min rep 3; Homo sapien... 9606 \n", "9 GSM2476006: 1.5 µM PF-067446846, 60 min, rep 1... 9606 \n", "10 GSM2476007: 1.5 µM PF-067446846, 60 min, rep 2... 9606 \n", "11 GSM2476008: 1.5 µM PF-067446846, 60 min, rep 3... 9606 \n", "12 GSM2476009: 0.3 µM PF-067446846, 60 min, rep 1... 9606 \n", "13 GSM2476010: 0.3 µM PF-067446846, 60 min, rep 2... 9606 \n", "14 GSM2476011: 0.3 µM PF-067446846, 60 min, rep 3... 9606 \n", "15 GSM2476012: vehicle, 60 min rep 1; Homo sapien... 9606 \n", "16 GSM2476013: vehicle, 60 min rep 2; Homo sapien... 9606 \n", "17 GSM2476014: vehicle, 60 min rep 3; Homo sapien... 9606 \n", "18 GSM2476015: 1.5 µM PF-067446846, 60 min, rep 4... 9606 \n", "19 GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; H... 9606 \n", "20 GSM2476017: 1.5 µM PF-067446846, 60 min, rep 5... 9606 \n", "21 GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; H... 9606 \n", "22 GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-s... 9606 \n", "23 GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Ho... 9606 \n", "24 GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-s... 9606 \n", "25 GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Ho... 9606 \n", "\n", " organism_name library_name library_strategy ... \\\n", "0 Homo sapiens OTHER ... \n", "1 Homo sapiens OTHER ... \n", "2 Homo sapiens OTHER ... \n", "3 Homo sapiens OTHER ... \n", "4 Homo sapiens OTHER ... \n", "5 Homo sapiens OTHER ... \n", "6 Homo sapiens OTHER ... \n", "7 Homo sapiens OTHER ... \n", "8 Homo sapiens OTHER ... \n", "9 Homo sapiens OTHER ... \n", "10 Homo sapiens OTHER ... \n", "11 Homo sapiens OTHER ... \n", "12 Homo sapiens OTHER ... \n", "13 Homo sapiens OTHER ... \n", "14 Homo sapiens OTHER ... \n", "15 Homo sapiens OTHER ... \n", "16 Homo sapiens OTHER ... \n", "17 Homo sapiens OTHER ... \n", "18 Homo sapiens OTHER ... \n", "19 Homo sapiens RNA-Seq ... \n", "20 Homo sapiens OTHER ... \n", "21 Homo sapiens RNA-Seq ... \n", "22 Homo sapiens OTHER ... \n", "23 Homo sapiens RNA-Seq ... \n", "24 Homo sapiens OTHER ... \n", "25 Homo sapiens RNA-Seq ... \n", "\n", " source_name cell line treatment time \\\n", "0 Huh7_1.5 µM PF-067446846_10 min_ribo-seq Huh7 10 min \n", "1 Huh7_1.5 µM PF-067446846_10 min_ribo-seq Huh7 10 min \n", "2 Huh7_1.5 µM PF-067446846_10 min_ribo-seq Huh7 10 min \n", "3 Huh7_0.3 µM PF-067446846_10 min_ribo-seq Huh7 10 min \n", "4 Huh7_0.3 µM PF-067446846_10 min_ribo-seq Huh7 10 min \n", "5 Huh7_0.3 µM PF-067446846_10 min_ribo-seq Huh7 10 min \n", "6 Huh7_vehicle_10 min_ribo-seq Huh7 10 min \n", "7 Huh7_vehicle_10 min_ribo-seq Huh7 10 min \n", "8 Huh7_vehicle_10 min_ribo-seq Huh7 10 min \n", "9 Huh7_1.5 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "10 Huh7_1.5 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "11 Huh7_1.5 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "12 Huh7_0.3 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "13 Huh7_0.3 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "14 Huh7_0.3 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "15 Huh7_vehicle_60 min_ribo-seq Huh7 60 min \n", "16 Huh7_vehicle_60 min_ribo-seq Huh7 60 min \n", "17 Huh7_vehicle_60 min_ribo-seq Huh7 60 min \n", "18 Huh7_1.5 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "19 Huh7_Veh_60 min_Ribo-seq Huh7 60 min \n", "20 Huh7_1.5 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "21 Huh7_vehcile_60 min_Ribo-seq Huh7 60 min \n", "22 Huh7_PF-06446846_60 min_mRNA-seq Huh7 60 min \n", "23 Huh7_vehicle_60 min_RNA-seq Huh7 60 min \n", "24 Huh7_PF-06446846_60 min_mRNA-seq Huh7 60 min \n", "25 Huh7_vehicle_60 min_RNA-seq Huh7 60 min \n", "\n", " library type ena_fastq_http \\\n", "0 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008... \n", "1 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009... \n", "2 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000... \n", "3 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001... \n", "4 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002... \n", "5 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003... \n", "6 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/004... \n", "7 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/005... \n", "8 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/006... \n", "9 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/007... \n", "10 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008... \n", "11 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009... \n", "12 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000... \n", "13 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001... \n", "14 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002... \n", "15 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003... \n", "16 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/004... \n", "17 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/005... \n", "18 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/006... \n", "19 Ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/007... \n", "20 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008... \n", "21 Ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009... \n", "22 mRNA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000... \n", "23 polyA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001... \n", "24 mRNA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002... \n", "25 polyA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003... \n", "\n", " ena_fastq_http_1 ena_fastq_http_2 \\\n", "0 \n", "1 \n", "2 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "8 \n", "9 \n", "10 \n", "11 \n", "12 \n", "13 \n", "14 \n", "15 \n", "16 \n", "17 \n", "18 \n", "19 \n", "20 \n", "21 \n", "22 \n", "23 \n", "24 \n", "25 \n", "\n", " ena_fastq_ftp ena_fastq_ftp_1 \\\n", "0 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "1 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "2 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "3 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "4 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "5 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "6 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "7 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "8 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "9 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "10 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "11 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "12 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "13 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "14 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "15 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "16 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "17 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "18 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "19 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "20 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "21 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "22 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "23 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "24 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "25 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "\n", " ena_fastq_ftp_2 \n", "0 \n", "1 \n", "2 \n", "3 \n", "4 \n", "5 \n", "6 \n", "7 \n", "8 \n", "9 \n", "10 \n", "11 \n", "12 \n", "13 \n", "14 \n", "15 \n", "16 \n", "17 \n", "18 \n", "19 \n", "20 \n", "21 \n", "22 \n", "23 \n", "24 \n", "25 \n", "\n", "[26 rows x 54 columns]" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df = db.sra_metadata(\"SRP098789\", detailed=True)\n", "df" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 1000 }, "colab_type": "code", "id": "QqjoVmskOegP", "outputId": "f8973741-bbf3-4988-aff7-ba09636a80e6" }, "outputs": [ { "data": { "text/html": [ "
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run_accessionstudy_accessionstudy_titleexperiment_accessionexperiment_titleexperiment_descorganism_taxidorganism_namelibrary_namelibrary_strategy...source_namecell linetreatment timelibrary typeena_fastq_httpena_fastq_http_1ena_fastq_http_2ena_fastq_ftpena_fastq_ftp_1ena_fastq_ftp_2
5SRR5227293SRP098789Selective stalling of human translation throug...SRX2536408GSM2476002: 0.3 µM PF-067446846, 10 min, rep 3...GSM2476002: 0.3 µM PF-067446846, 10 min, rep 3...9606Homo sapiens<NA>OTHER...Huh7_0.3 µM PF-067446846_10 min_ribo-seqHuh710 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
6SRR5227294SRP098789Selective stalling of human translation throug...SRX2536409GSM2476003: vehicle, 10 min rep 1; Homo sapien...GSM2476003: vehicle, 10 min rep 1; Homo sapien...9606Homo sapiens<NA>OTHER...Huh7_vehicle_10 min_ribo-seqHuh710 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/004...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
7SRR5227295SRP098789Selective stalling of human translation throug...SRX2536410GSM2476004: vehicle, 10 min rep 2; Homo sapien...GSM2476004: vehicle, 10 min rep 2; Homo sapien...9606Homo sapiens<NA>OTHER...Huh7_vehicle_10 min_ribo-seqHuh710 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/005...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
8SRR5227296SRP098789Selective stalling of human translation throug...SRX2536411GSM2476005: vehicle, 10 min rep 3; Homo sapien...GSM2476005: vehicle, 10 min rep 3; Homo sapien...9606Homo sapiens<NA>OTHER...Huh7_vehicle_10 min_ribo-seqHuh710 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/006...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
9SRR5227297SRP098789Selective stalling of human translation throug...SRX2536412GSM2476006: 1.5 µM PF-067446846, 60 min, rep 1...GSM2476006: 1.5 µM PF-067446846, 60 min, rep 1...9606Homo sapiens<NA>OTHER...Huh7_1.5 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/007...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
10SRR5227298SRP098789Selective stalling of human translation throug...SRX2536413GSM2476007: 1.5 µM PF-067446846, 60 min, rep 2...GSM2476007: 1.5 µM PF-067446846, 60 min, rep 2...9606Homo sapiens<NA>OTHER...Huh7_1.5 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
11SRR5227299SRP098789Selective stalling of human translation throug...SRX2536414GSM2476008: 1.5 µM PF-067446846, 60 min, rep 3...GSM2476008: 1.5 µM PF-067446846, 60 min, rep 3...9606Homo sapiens<NA>OTHER...Huh7_1.5 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
12SRR5227300SRP098789Selective stalling of human translation throug...SRX2536415GSM2476009: 0.3 µM PF-067446846, 60 min, rep 1...GSM2476009: 0.3 µM PF-067446846, 60 min, rep 1...9606Homo sapiens<NA>OTHER...Huh7_0.3 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
13SRR5227301SRP098789Selective stalling of human translation throug...SRX2536416GSM2476010: 0.3 µM PF-067446846, 60 min, rep 2...GSM2476010: 0.3 µM PF-067446846, 60 min, rep 2...9606Homo sapiens<NA>OTHER...Huh7_0.3 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
14SRR5227302SRP098789Selective stalling of human translation throug...SRX2536417GSM2476011: 0.3 µM PF-067446846, 60 min, rep 3...GSM2476011: 0.3 µM PF-067446846, 60 min, rep 3...9606Homo sapiens<NA>OTHER...Huh7_0.3 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
15SRR5227303SRP098789Selective stalling of human translation throug...SRX2536418GSM2476012: vehicle, 60 min rep 1; Homo sapien...GSM2476012: vehicle, 60 min rep 1; Homo sapien...9606Homo sapiens<NA>OTHER...Huh7_vehicle_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
16SRR5227304SRP098789Selective stalling of human translation throug...SRX2536419GSM2476013: vehicle, 60 min rep 2; Homo sapien...GSM2476013: vehicle, 60 min rep 2; Homo sapien...9606Homo sapiens<NA>OTHER...Huh7_vehicle_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/004...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
17SRR5227305SRP098789Selective stalling of human translation throug...SRX2536420GSM2476014: vehicle, 60 min rep 3; Homo sapien...GSM2476014: vehicle, 60 min rep 3; Homo sapien...9606Homo sapiens<NA>OTHER...Huh7_vehicle_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/005...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
18SRR5227306SRP098789Selective stalling of human translation throug...SRX2536421GSM2476015: 1.5 µM PF-067446846, 60 min, rep 4...GSM2476015: 1.5 µM PF-067446846, 60 min, rep 4...9606Homo sapiens<NA>OTHER...Huh7_1.5 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/006...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
19SRR5227307SRP098789Selective stalling of human translation throug...SRX2536422GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; H...GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; H...9606Homo sapiens<NA>RNA-Seq...Huh7_Veh_60 min_Ribo-seqHuh760 minRibo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/007...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
20SRR5227308SRP098789Selective stalling of human translation throug...SRX2536423GSM2476017: 1.5 µM PF-067446846, 60 min, rep 5...GSM2476017: 1.5 µM PF-067446846, 60 min, rep 5...9606Homo sapiens<NA>OTHER...Huh7_1.5 µM PF-067446846_60 min_ribo-seqHuh760 minribo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
21SRR5227309SRP098789Selective stalling of human translation throug...SRX2536424GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; H...GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; H...9606Homo sapiens<NA>RNA-Seq...Huh7_vehcile_60 min_Ribo-seqHuh760 minRibo-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
22SRR5227310SRP098789Selective stalling of human translation throug...SRX2536425GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-s...GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-s...9606Homo sapiens<NA>OTHER...Huh7_PF-06446846_60 min_mRNA-seqHuh760 minmRNA-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
23SRR5227311SRP098789Selective stalling of human translation throug...SRX2536426GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Ho...GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Ho...9606Homo sapiens<NA>RNA-Seq...Huh7_vehicle_60 min_RNA-seqHuh760 minpolyA-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
24SRR5227312SRP098789Selective stalling of human translation throug...SRX2536427GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-s...GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-s...9606Homo sapiens<NA>OTHER...Huh7_PF-06446846_60 min_mRNA-seqHuh760 minmRNA-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
25SRR5227313SRP098789Selective stalling of human translation throug...SRX2536428GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Ho...GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Ho...9606Homo sapiens<NA>RNA-Seq...Huh7_vehicle_60 min_RNA-seqHuh760 minpolyA-seqhttp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003...<NA><NA>era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/...<NA><NA>
\n", "

21 rows × 54 columns

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" ], "text/plain": [ " run_accession study_accession \\\n", "5 SRR5227293 SRP098789 \n", "6 SRR5227294 SRP098789 \n", "7 SRR5227295 SRP098789 \n", "8 SRR5227296 SRP098789 \n", "9 SRR5227297 SRP098789 \n", "10 SRR5227298 SRP098789 \n", "11 SRR5227299 SRP098789 \n", "12 SRR5227300 SRP098789 \n", "13 SRR5227301 SRP098789 \n", "14 SRR5227302 SRP098789 \n", "15 SRR5227303 SRP098789 \n", "16 SRR5227304 SRP098789 \n", "17 SRR5227305 SRP098789 \n", "18 SRR5227306 SRP098789 \n", "19 SRR5227307 SRP098789 \n", "20 SRR5227308 SRP098789 \n", "21 SRR5227309 SRP098789 \n", "22 SRR5227310 SRP098789 \n", "23 SRR5227311 SRP098789 \n", "24 SRR5227312 SRP098789 \n", "25 SRR5227313 SRP098789 \n", "\n", " study_title experiment_accession \\\n", "5 Selective stalling of human translation throug... SRX2536408 \n", "6 Selective stalling of human translation throug... SRX2536409 \n", "7 Selective stalling of human translation throug... SRX2536410 \n", "8 Selective stalling of human translation throug... SRX2536411 \n", "9 Selective stalling of human translation throug... SRX2536412 \n", "10 Selective stalling of human translation throug... SRX2536413 \n", "11 Selective stalling of human translation throug... SRX2536414 \n", "12 Selective stalling of human translation throug... SRX2536415 \n", "13 Selective stalling of human translation throug... SRX2536416 \n", "14 Selective stalling of human translation throug... SRX2536417 \n", "15 Selective stalling of human translation throug... SRX2536418 \n", "16 Selective stalling of human translation throug... SRX2536419 \n", "17 Selective stalling of human translation throug... SRX2536420 \n", "18 Selective stalling of human translation throug... SRX2536421 \n", "19 Selective stalling of human translation throug... SRX2536422 \n", "20 Selective stalling of human translation throug... SRX2536423 \n", "21 Selective stalling of human translation throug... SRX2536424 \n", "22 Selective stalling of human translation throug... SRX2536425 \n", "23 Selective stalling of human translation throug... SRX2536426 \n", "24 Selective stalling of human translation throug... SRX2536427 \n", "25 Selective stalling of human translation throug... SRX2536428 \n", "\n", " experiment_title \\\n", "5 GSM2476002: 0.3 µM PF-067446846, 10 min, rep 3... \n", "6 GSM2476003: vehicle, 10 min rep 1; Homo sapien... \n", "7 GSM2476004: vehicle, 10 min rep 2; Homo sapien... \n", "8 GSM2476005: vehicle, 10 min rep 3; Homo sapien... \n", "9 GSM2476006: 1.5 µM PF-067446846, 60 min, rep 1... \n", "10 GSM2476007: 1.5 µM PF-067446846, 60 min, rep 2... \n", "11 GSM2476008: 1.5 µM PF-067446846, 60 min, rep 3... \n", "12 GSM2476009: 0.3 µM PF-067446846, 60 min, rep 1... \n", "13 GSM2476010: 0.3 µM PF-067446846, 60 min, rep 2... \n", "14 GSM2476011: 0.3 µM PF-067446846, 60 min, rep 3... \n", "15 GSM2476012: vehicle, 60 min rep 1; Homo sapien... \n", "16 GSM2476013: vehicle, 60 min rep 2; Homo sapien... \n", "17 GSM2476014: vehicle, 60 min rep 3; Homo sapien... \n", "18 GSM2476015: 1.5 µM PF-067446846, 60 min, rep 4... \n", "19 GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; H... \n", "20 GSM2476017: 1.5 µM PF-067446846, 60 min, rep 5... \n", "21 GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; H... \n", "22 GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-s... \n", "23 GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Ho... \n", "24 GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-s... \n", "25 GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Ho... \n", "\n", " experiment_desc organism_taxid \\\n", "5 GSM2476002: 0.3 µM PF-067446846, 10 min, rep 3... 9606 \n", "6 GSM2476003: vehicle, 10 min rep 1; Homo sapien... 9606 \n", "7 GSM2476004: vehicle, 10 min rep 2; Homo sapien... 9606 \n", "8 GSM2476005: vehicle, 10 min rep 3; Homo sapien... 9606 \n", "9 GSM2476006: 1.5 µM PF-067446846, 60 min, rep 1... 9606 \n", "10 GSM2476007: 1.5 µM PF-067446846, 60 min, rep 2... 9606 \n", "11 GSM2476008: 1.5 µM PF-067446846, 60 min, rep 3... 9606 \n", "12 GSM2476009: 0.3 µM PF-067446846, 60 min, rep 1... 9606 \n", "13 GSM2476010: 0.3 µM PF-067446846, 60 min, rep 2... 9606 \n", "14 GSM2476011: 0.3 µM PF-067446846, 60 min, rep 3... 9606 \n", "15 GSM2476012: vehicle, 60 min rep 1; Homo sapien... 9606 \n", "16 GSM2476013: vehicle, 60 min rep 2; Homo sapien... 9606 \n", "17 GSM2476014: vehicle, 60 min rep 3; Homo sapien... 9606 \n", "18 GSM2476015: 1.5 µM PF-067446846, 60 min, rep 4... 9606 \n", "19 GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; H... 9606 \n", "20 GSM2476017: 1.5 µM PF-067446846, 60 min, rep 5... 9606 \n", "21 GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; H... 9606 \n", "22 GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-s... 9606 \n", "23 GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Ho... 9606 \n", "24 GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-s... 9606 \n", "25 GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Ho... 9606 \n", "\n", " organism_name library_name library_strategy ... \\\n", "5 Homo sapiens OTHER ... \n", "6 Homo sapiens OTHER ... \n", "7 Homo sapiens OTHER ... \n", "8 Homo sapiens OTHER ... \n", "9 Homo sapiens OTHER ... \n", "10 Homo sapiens OTHER ... \n", "11 Homo sapiens OTHER ... \n", "12 Homo sapiens OTHER ... \n", "13 Homo sapiens OTHER ... \n", "14 Homo sapiens OTHER ... \n", "15 Homo sapiens OTHER ... \n", "16 Homo sapiens OTHER ... \n", "17 Homo sapiens OTHER ... \n", "18 Homo sapiens OTHER ... \n", "19 Homo sapiens RNA-Seq ... \n", "20 Homo sapiens OTHER ... \n", "21 Homo sapiens RNA-Seq ... \n", "22 Homo sapiens OTHER ... \n", "23 Homo sapiens RNA-Seq ... \n", "24 Homo sapiens OTHER ... \n", "25 Homo sapiens RNA-Seq ... \n", "\n", " source_name cell line treatment time \\\n", "5 Huh7_0.3 µM PF-067446846_10 min_ribo-seq Huh7 10 min \n", "6 Huh7_vehicle_10 min_ribo-seq Huh7 10 min \n", "7 Huh7_vehicle_10 min_ribo-seq Huh7 10 min \n", "8 Huh7_vehicle_10 min_ribo-seq Huh7 10 min \n", "9 Huh7_1.5 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "10 Huh7_1.5 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "11 Huh7_1.5 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "12 Huh7_0.3 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "13 Huh7_0.3 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "14 Huh7_0.3 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "15 Huh7_vehicle_60 min_ribo-seq Huh7 60 min \n", "16 Huh7_vehicle_60 min_ribo-seq Huh7 60 min \n", "17 Huh7_vehicle_60 min_ribo-seq Huh7 60 min \n", "18 Huh7_1.5 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "19 Huh7_Veh_60 min_Ribo-seq Huh7 60 min \n", "20 Huh7_1.5 µM PF-067446846_60 min_ribo-seq Huh7 60 min \n", "21 Huh7_vehcile_60 min_Ribo-seq Huh7 60 min \n", "22 Huh7_PF-06446846_60 min_mRNA-seq Huh7 60 min \n", "23 Huh7_vehicle_60 min_RNA-seq Huh7 60 min \n", "24 Huh7_PF-06446846_60 min_mRNA-seq Huh7 60 min \n", "25 Huh7_vehicle_60 min_RNA-seq Huh7 60 min \n", "\n", " library type ena_fastq_http \\\n", "5 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003... \n", "6 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/004... \n", "7 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/005... \n", "8 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/006... \n", "9 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/007... \n", "10 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008... \n", "11 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009... \n", "12 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000... \n", "13 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001... \n", "14 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002... \n", "15 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003... \n", "16 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/004... \n", "17 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/005... \n", "18 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/006... \n", "19 Ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/007... \n", "20 ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008... \n", "21 Ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009... \n", "22 mRNA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000... \n", "23 polyA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001... \n", "24 mRNA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002... \n", "25 polyA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003... \n", "\n", " ena_fastq_http_1 ena_fastq_http_2 \\\n", "5 \n", "6 \n", "7 \n", "8 \n", "9 \n", "10 \n", "11 \n", "12 \n", "13 \n", "14 \n", "15 \n", "16 \n", "17 \n", "18 \n", "19 \n", "20 \n", "21 \n", "22 \n", "23 \n", "24 \n", "25 \n", "\n", " ena_fastq_ftp ena_fastq_ftp_1 \\\n", "5 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "6 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "7 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "8 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "9 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "10 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "11 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "12 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "13 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "14 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "15 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "16 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "17 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "18 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "19 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "20 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "21 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "22 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "23 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "24 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "25 era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... \n", "\n", " ena_fastq_ftp_2 \n", "5 \n", "6 \n", "7 \n", "8 \n", "9 \n", "10 \n", "11 \n", "12 \n", "13 \n", "14 \n", "15 \n", "16 \n", "17 \n", "18 \n", "19 \n", "20 \n", "21 \n", "22 \n", "23 \n", "24 \n", "25 \n", "\n", "[21 rows x 54 columns]" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# randomply split into two dataframes\n", "df1, df2 = df.iloc[:5, :], df.iloc[5:, :]\n", "\n", "df2" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "colab": {}, "colab_type": "code", "id": "Wbelu2eNO4d_" }, "outputs": [], "source": [ "def single_download(df_single):\n", " db.download(df=df_single, skip_confirmation=True)" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "colab": {}, "colab_type": "code", "id": "r2TzSAZ0PSIe" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Checking download URLs\n", "Checking download URLs\n", "The following files will be downloaded: \n", "\n", "run_accession study_accession experiment_accession public_url download_url out_dir filesize\n", "SRR5227288 SRP098789 SRX2536403 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR005/227/SRR5227288/SRR5227288.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227288/SRR5227288.sra /data/github/pysradb/notebooks/pysradb_downloads 533.5 MB\n", "SRR5227289 SRP098789 SRX2536404 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR005/227/SRR5227289/SRR5227289.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227289/SRR5227289.sra /data/github/pysradb/notebooks/pysradb_downloads 603.2 MB\n", "SRR5227290 SRP098789 SRX2536405 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR005/227/SRR5227290/SRR5227290.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227290/SRR5227290.sra /data/github/pysradb/notebooks/pysradb_downloads 586.1 MB\n", "SRR5227291 SRP098789 SRX2536406 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227291.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227291/SRR5227291.sra /data/github/pysradb/notebooks/pysradb_downloads 521.5 MB\n", "SRR5227292 SRP098789 SRX2536407 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227292.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227292/SRR5227292.sra /data/github/pysradb/notebooks/pysradb_downloads 871.3 MB\n", "\n", "\n", "Total size: 3.1 GB\n", "\n", "\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ " 0%| | 0/5 [00:00