radusuciu/ip2api

A simple interface for IP2 written in Python 3.

Setting up environment from scratch with virtualenv in Linux

virtualenv env
source env/bin/activate
pip install -r requirements.txt

Usage

import json
from ip2api import IP2, IP2Experiment, IP2Job

# authenticate
ip2 = IP2(ip2_url='http://goldfish.scripps.edu', username=USERNAME)
ip2.login(PASSWORD)

# Get a list of projects
print(ip2.projects)

# Get a project that already exists, and do stuff
project = ip2.get_project('my_project')
print(project.experiments)


# create a new experiment and upload spectra
new_experiment = IP2Experiment(ip2, project, 'my_experiment')
new_experiment.create()
new_experiment.upload_files(['test1.raw', 'test2.raw'])

database = ip2.get_database('UniProt_Human_Cravattlab_nonredundant2_98id_11-05-2012_reversed.fasta')

with open('params/silac.json') as f:
    params = json.loads(f.read())

job = new_experiment.prolucid_search(params, database)
print(job)
job.update()
print(job)

# Get an experiment by name
experiment = ip2.get_experiment('my_project', 'my_experiment')

Running tests

# IP2 requires authentication, so even for running tests you must provide a username and password.
python tests/test_ip2api.py IP2_USERNAME IP2_PASSWORD