For development, clone or download-and-extract the repository. Then run pip install -e . from the repository's root directory. The -e flag specifies editable mode, so updating the source updates your installation.
The current master branch can also be installed directly from GitHub using:
pip install git+git://github.com/idrdex/star_api.git@master
Users must manually create a file at starapi/db_conf.py with the following:
DB_PARAMATERS = """host='star.cwxuiazqnkkn.us-west-2.rds.amazonaws.com'
dbname='star'
user='XXXXXXXXXX'
password='XXXXXXXXXX'"""Contact @idrdex for this information.
from starapi.main import get_annotations
from starapi.analysis import combat, perform_analysis
from starapi import conf
conf.configure('./')
analysis = EasyDict(
analysis_name="severe_dengue_top",
case_query="DHF=='DHF' or DSS=='DSS'",
control_query="DF=='DF'",
modifier_query="Dengue_Acute=='Dengue_Acute'",
min_samples=3
)
nperm = 3
basename = "%s.%s_perm"%(analysis.analysis_name, nperm)
df, fc, results, permutations = perform_analysis(
analysis=analysis,
impute=False,
nperm=nperm,
mygene_filter=None,
debug=basename
)