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| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "This notebook computes on the freely available GTEX version 8 files on Amazon AWS using the Seven Bridges Cancer Genomics Cloud WES service. \n", | ||
| "\n", | ||
| "In this case the DRS ids of the GTEX files are available via a client which acccess a local manifest file. The manifest file is obtained from Anvil as follows.\n", | ||
| "https://anvilproject.org/learn/reference/gtex-v8-free-egress-instructions\n", | ||
| "\n", | ||
| "Rather than use the Gen3 Downloader described in the egress instructions, this example uses the Anvil DRS service to obtain URLs which can be passed to the Seven Bridges CGC WES Service.\n", | ||
| "\n", | ||
| "The following step demonstrates a query run against that file. " | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 1, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from fasp.runner import FASPRunner\n", | ||
| "\n", | ||
| "# The implementations we're using\n", | ||
| "from fasp.workflow import DNAStackWESClient\n", | ||
| "from fasp.loc import anvilDRSClient\n", | ||
| "from fasp.search import Gen3ManifestClient\n", | ||
| "\n", | ||
| "faspRunner = FASPRunner(program='GTEXExample')\n", | ||
| "\n", | ||
| "# Step 1 - Discovery\n", | ||
| "# query for relevant DRS objects\n", | ||
| "searchClient = Gen3ManifestClient('../fasp/data/gtex/gtex-cram-manifest.json')\n", | ||
| "res = searchClient.runQuery(3)\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 2, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "{'access_methods': [{'access_id': 'gs',\n", | ||
| " 'access_url': {'url': 'gs://fc-secure-ff8156a3-ddf3-42e4-9211-0fd89da62108/GTEx_Analysis_2017-06-05_v8_WGS_CRAM_files/GTEX-1B98T-0004-SM-7J38T.cram'},\n", | ||
| " 'region': '',\n", | ||
| " 'type': 'gs'},\n", | ||
| " {'access_id': 's3',\n", | ||
| " 'access_url': {'url': 's3://AnVIL/GTEx_Analysis_2017-06-05_v8_WGS_CRAM_files/GTEX-1B98T-0004-SM-7J38T.cram'},\n", | ||
| " 'region': '',\n", | ||
| " 'type': 's3'}],\n", | ||
| " 'aliases': [],\n", | ||
| " 'checksums': [{'checksum': 'cfd2f4cde4aa3e0cf9f726f0c1255fcd',\n", | ||
| " 'type': 'md5'}],\n", | ||
| " 'contents': [],\n", | ||
| " 'created_time': '2020-07-08T18:53:27.860156',\n", | ||
| " 'description': None,\n", | ||
| " 'form': 'object',\n", | ||
| " 'id': 'dg.ANV0/ed9ac9ae-02da-4e97-93da-ad86aa77d227',\n", | ||
| " 'mime_type': 'application/json',\n", | ||
| " 'name': 'GTEX-1B98T-0004-SM-7J38T.cram',\n", | ||
| " 'self_uri': 'drs://gen3.theanvil.io/dg.ANV0/ed9ac9ae-02da-4e97-93da-ad86aa77d227',\n", | ||
| " 'size': 38379493977,\n", | ||
| " 'updated_time': '2020-07-08T18:53:27.860163',\n", | ||
| " 'version': '64acd5a6'}" | ||
| ] | ||
| }, | ||
| "execution_count": 2, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "drsClient = anvilDRSClient('~/.keys/anvil_credentials.json', access_id='gs')\n", | ||
| "drsClient.getObject(res[2][1])" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 3, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "url = drsClient.getAccessURL(res[2][1])" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 4, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "Running query\n", | ||
| "3\n", | ||
| "subject=GTEX-1GTWX-0001-SM-7J3A5.cram, drsID=dg.ANV0/76bb893d-12da-41ca-8828-ff89551d3e15\n", | ||
| "workflow submitted, run:2f73492e-d109-4e1a-b2be-9950deae9890\n", | ||
| "subject=GTEX-14PQA-0003-SM-7DLH4.cram, drsID=dg.ANV0/66352de8-4b50-4cae-881d-b76d03df5ac8\n", | ||
| "workflow submitted, run:6c63ef08-e61b-43a8-ab07-7975a98bdbb8\n", | ||
| "subject=GTEX-1B98T-0004-SM-7J38T.cram, drsID=dg.ANV0/ed9ac9ae-02da-4e97-93da-ad86aa77d227\n", | ||
| "workflow submitted, run:1d764abd-5c8f-4c89-ad2b-26a43b2025f1\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "settings = faspRunner.settings\n", | ||
| "wesClient = DNAStackWESClient('~/.keys/dnastack_wes_credentials.json')\n", | ||
| "\n", | ||
| "faspRunner.configure(searchClient, drsClient, wesClient)\n", | ||
| "\n", | ||
| "runList = faspRunner.runQuery(3, 'Anvil GTEX DRS to DNAStack WES')" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 7, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "2f73492e-d109-4e1a-b2be-9950deae9890 RUNNING\n", | ||
| "6c63ef08-e61b-43a8-ab07-7975a98bdbb8 RUNNING\n", | ||
| "1d764abd-5c8f-4c89-ad2b-26a43b2025f1 RUNNING\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "for run in runList:\n", | ||
| " print(run['run_id'], wesClient.getTaskStatus(run['run_id']))" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 8, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "[{'subject': 'GTEX-1GTWX-0001-SM-7J3A5.cram', 'run_id': '2f73492e-d109-4e1a-b2be-9950deae9890'}, {'subject': 'GTEX-14PQA-0003-SM-7DLH4.cram', 'run_id': '6c63ef08-e61b-43a8-ab07-7975a98bdbb8'}, {'subject': 'GTEX-1B98T-0004-SM-7J38T.cram', 'run_id': '1d764abd-5c8f-4c89-ad2b-26a43b2025f1'}]\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "print (runList)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "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": "3.7.3" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 4 | ||
| } |
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