naga-gwas-rest 0.7.1

REST service for Network Assisted Genomic Analysis (NAGA)

naga-gwas-rest

REST service for Network Assisted Genomic Analysis (NAGA)

For more information please click here to visit our wiki

This service is currently running here: http://nbgwas.ucsd.edu

Compatibility

• Tested with Python 3.6 in Anaconda

Dependencies to run

• naga-gwas

• ndex2

• python-daemon

• flask

• flask-restplus

• numpy

Additional dependencies to build

• GNU make

• wheel

• setuptools

Installation

It is highly reccommended one use Anaconda for Python environment

git clone https://github.com/idekerlab/naga-gwas-rest.git
cd naga-gwas-rest
make install

Running service in development mode

NOTE: Example below runs the REST service and not the task runner.

# It is assumed the application has been installed as described above
export FLASK_APP=nbgwas_rest
flask run # --host=0.0.0.0 can be added to allow all access from interfaces

# Service will be running on http://localhost:5000

# NOTE: To have tasks processed naga_taskrunner.py must be started in
# another terminal

Click here for information on launching service via Vagrant VM

Example usage of service

Below is a small script that leverages the nbgwas_rest service to run NAGA on the compressed nagadata/schizophrenia.txt.gz passed into the script on the command line

#!/usr/bin/env python

import sys
import gzip
import time
import requests

# pass the gzipped schizophrenia.txt.gz
networkfile = sys.argv[1]

# set parameters
data_dict = {}
data_dict['protein_coding']='hg18'
data_dict['window']=10000
data_dict['ndex']='f93f402c-86d4-11e7-a10d-0ac135e8bacf'

# set snp file
files = {'snp_level_summary': gzip.open(networkfile, 'rb')}
url = 'http://nbgwas.ucsd.edu/rest/v1/snp_analyzer'
r = requests.post(url, data=data_dict, files=files,
                  timeout=30)

# If successful the previous POST will return 202
if r.status_code != 202:
    sys.stderr.write('Submission failed with code: ' + str(r.status_code) +
                     '\n')
    sys.stderr.write('Message: ' + str(r.text) + '\n')
    sys.exit(1)

# If successful Location will be set to a URL that can
# be polled for result
if 'Location' not in r.headers:
    sys.stderr.write('Expected Location in Header, ' +
                     'but its not there: ' + str(r.headers) + '\n')
    sys.exit(2)

resulturl = r.headers['Location']
getres = requests.get(resulturl, timeout=30)
json_res = getres.json()
while getres.status_code != 200 or json_res['status'] == 'submitted' or json_res['status'] == 'processing':
   sys.stderr.write('.')
   sys.stderr.flush()
   time.sleep(5)
   getres = requests.get(resulturl, timeout=30)
   json_res = getres.json()

sys.stderr.write('\n')
sys.stdout.write(str(json_res) + '\n')

Assuming the above is saved in a file named foo.py and run from base directory of this source tree

./foo.py nagadata/schizophrenia.txt.gz

Example output:

{'result': {'A1BG': 1.818739214334769, 'A1CF': 2.9679830980888413,
'A2M': 3.9294999566765174, 'A2ML1': 1.4379620790934335, 'A3GALT2': 1.9918435374785632,
'A4GALT': 1.8734641163972634, 'A4GNT': 1.335302470858104, 'AAAS': 2.384799543926567,
'AACS': 2.965792987307328, 'AADAC': 1.455957465785784, 'AADACL2': 1.0156608351922358,
'AADACL3': 0.895944981993654, 'AADACL4': 1.2458363441128992, 'AADAT': 2.689141678947707,
'AAED1': 0.12364477699188797, 'AAGAB': 0.14237051805828474, 'AAK1': 5.652340641567231,
'AAMDC': 0.1647736242197245, 'AAMP': 3.2927511707526884, 'AANAT': 5.654764562774087,
'AAR2': 0.9427896961129361,
.
.
, 'status': 'done'}

Bugs

Please report them here

Acknowledgements

• Original implementation by Samson Fong

• Initial template created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.7.1 (2021-02-03)

• Minor changes to enable naga_taskrunner.py to run as a systemd service on centos7 boxes

0.7.0 (2019-07-01)

• Added dm6 in list of valid protein coding region files

0.6.0 (2019-05-06)

• Added mm10 and rn6 in list of valid protein coding region files

0.5.0 (2019-03-07)

• Replace infinite heat values returned from NAGA bug issue #24

• Add naga version used in processing to result json issue #23

• Rename to naga-gwas-rest issue #22

• Add input parameters snp_analyzer/get endpoint enhancement issue #20

• Modify naga_taskrunner.py to run in a daemon mode issue #3

0.4.1 (2018-12-20)

• Replace Association with Analysis in REST service description bug issue #19

0.4.0 (2018-12-19)

• Enabled DELETE rest endpoint issue #16

• Fixed problems including numpy and running under apache modwsgi bug issue #15

• nbgwas_taskrunner.py should remove snp level summary file after job runs issue #5

0.1.1 (2018-11-30)

• First release onto github