{
"info": {
"author": "Chris Churas",
"author_email": "churas.camera@gmail.com",
"bugtrack_url": null,
"classifiers": [
"Development Status :: 2 - Pre-Alpha",
"Intended Audience :: Developers",
"License :: OSI Approved :: BSD License",
"Natural Language :: English",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.4",
"Programming Language :: Python :: 3.5",
"Programming Language :: Python :: 3.6",
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"description": "==============\nnaga-gwas-rest\n==============\n\n\n.. image:: https://img.shields.io/pypi/v/naga-gwas-rest.svg\n :target: https://pypi.python.org/pypi/naga-gwas-rest\n\n.. image:: https://img.shields.io/travis/idekerlab/naga-gwas-rest.svg\n :target: https://travis-ci.org/idekerlab/naga-gwas-rest\n\n\n\n\nREST service for `Network Assisted Genomic Analysis (NAGA) `_\n\n`For more information please click here to visit our wiki `_\n\nThis service is currently running here: http://nbgwas.ucsd.edu\n\nCompatibility\n-------------\n\n * Tested with Python 3.6 in Anaconda_\n\nDependencies to run\n-------------------\n\n * `naga-gwas `_\n * `ndex2 `_\n * `python-daemon `_\n * `flask `_\n * `flask-restplus `_\n * `numpy `_\n\nAdditional dependencies to build\n--------------------------------\n\n * GNU make\n * `wheel `_\n * `setuptools `_\n\n\nInstallation\n------------\n\nIt is highly reccommended one use `Anaconda `_ for Python environment\n\n.. code:: bash\n\n git clone https://github.com/idekerlab/naga-gwas-rest.git\n cd naga-gwas-rest\n make install\n\nRunning service in development mode\n-----------------------------------\n\n\n**NOTE:** Example below runs the REST service and not the task runner.\n\n.. code:: bash\n\n # It is assumed the application has been installed as described above\n export FLASK_APP=nbgwas_rest\n flask run # --host=0.0.0.0 can be added to allow all access from interfaces\n\n # Service will be running on http://localhost:5000\n\n # NOTE: To have tasks processed naga_taskrunner.py must be started in\n # another terminal\n\n\n`Click here for information on launching service via Vagrant VM `_\n\n\nExample usage of service\n------------------------\n\nBelow is a small script that leverages the nbgwas_rest service to run NAGA on the\ncompressed **nagadata/schizophrenia.txt.gz** passed into the script on the command line\n\n.. code:: bash\n\n #!/usr/bin/env python\n\n import sys\n import gzip\n import time\n import requests\n\n # pass the gzipped schizophrenia.txt.gz\n networkfile = sys.argv[1]\n\n # set parameters\n data_dict = {}\n data_dict['protein_coding']='hg18'\n data_dict['window']=10000\n data_dict['ndex']='f93f402c-86d4-11e7-a10d-0ac135e8bacf'\n\n # set snp file\n files = {'snp_level_summary': gzip.open(networkfile, 'rb')}\n url = 'http://nbgwas.ucsd.edu/rest/v1/snp_analyzer'\n r = requests.post(url, data=data_dict, files=files,\n timeout=30)\n\n # If successful the previous POST will return 202\n if r.status_code != 202:\n sys.stderr.write('Submission failed with code: ' + str(r.status_code) +\n '\\n')\n sys.stderr.write('Message: ' + str(r.text) + '\\n')\n sys.exit(1)\n\n # If successful Location will be set to a URL that can\n # be polled for result\n if 'Location' not in r.headers:\n sys.stderr.write('Expected Location in Header, ' +\n 'but its not there: ' + str(r.headers) + '\\n')\n sys.exit(2)\n\n resulturl = r.headers['Location']\n getres = requests.get(resulturl, timeout=30)\n json_res = getres.json()\n while getres.status_code != 200 or json_res['status'] == 'submitted' or json_res['status'] == 'processing':\n sys.stderr.write('.')\n sys.stderr.flush()\n time.sleep(5)\n getres = requests.get(resulturl, timeout=30)\n json_res = getres.json()\n\n sys.stderr.write('\\n')\n sys.stdout.write(str(json_res) + '\\n')\n\nAssuming the above is saved in a file named **foo.py** and run from base directory of this source tree\n\n\n.. code:: bash\n\n ./foo.py nagadata/schizophrenia.txt.gz\n\n\nExample output:\n\n.. code:: bash\n\n {'result': {'A1BG': 1.818739214334769, 'A1CF': 2.9679830980888413,\n 'A2M': 3.9294999566765174, 'A2ML1': 1.4379620790934335, 'A3GALT2': 1.9918435374785632,\n 'A4GALT': 1.8734641163972634, 'A4GNT': 1.335302470858104, 'AAAS': 2.384799543926567,\n 'AACS': 2.965792987307328, 'AADAC': 1.455957465785784, 'AADACL2': 1.0156608351922358,\n 'AADACL3': 0.895944981993654, 'AADACL4': 1.2458363441128992, 'AADAT': 2.689141678947707,\n 'AAED1': 0.12364477699188797, 'AAGAB': 0.14237051805828474, 'AAK1': 5.652340641567231,\n 'AAMDC': 0.1647736242197245, 'AAMP': 3.2927511707526884, 'AANAT': 5.654764562774087,\n 'AAR2': 0.9427896961129361,\n .\n .\n , 'status': 'done'}\n\nBugs\n-----\n\nPlease report them `here `_\n\nAcknowledgements\n----------------\n\n* Original implementation by `Samson Fong `_\n\n* Initial template created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n.. _Anaconda: https://www.anaconda.com/\n\n\n=======\nHistory\n=======\n0.7.0 (2019-07-01)\n------------------\n\n* Added dm6 in list of valid protein coding region files\n\n0.6.0 (2019-05-06)\n------------------\n\n* Added mm10 and rn6 in list of valid protein coding region files\n\n0.5.0 (2019-03-07)\n------------------\n\n* Replace infinite heat values returned from NAGA bug\n `issue #24 `_\n\n* Add naga version used in processing to result json\n `issue #23 `_\n\n* Rename to naga-gwas-rest\n `issue #22 `_\n\n* Add input parameters snp_analyzer/get endpoint enhancement\n `issue #20 `_\n\n* Modify naga_taskrunner.py to run in a daemon mode\n `issue #3 `_\n\n\n0.4.1 (2018-12-20)\n------------------\n\n* Replace Association with Analysis in REST service description bug\n `issue #19 `_\n\n0.4.0 (2018-12-19)\n------------------\n\n* Enabled DELETE rest endpoint `issue #16 `_\n\n* Fixed problems including numpy and running under apache modwsgi bug\n `issue #15 `_\n\n* nbgwas_taskrunner.py should remove snp level summary file after job runs\n `issue #5 `_\n\n0.1.1 (2018-11-30)\n------------------\n\n* First release onto github\n\n\n",
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