/
interAssay.py
45 lines (38 loc) · 1.4 KB
/
interAssay.py
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"""
Function: interAssay
This script generates a distribution of differencs observed between two experiments assessing the potency of identical compounds and targets
--------------------
Felix Kruger
momo.sander@googlemail.com
"""
def interAssay():
import queryDevice
import mkDict
import queries
import writePairs
import os
import addProperties
import readIds
import string
import yaml
# Read config file.
paramFile = open('gla.yaml')
params = yaml.safe_load(paramFile)
species = params['species']
# Get information for all relevant activities from ChEMBL.
for spec in species:
specName = string.replace(spec, ' ','_')
dictFile = "data/inter_compDict_%s_%s.pkl" % (specName, params['release'])
results = "data/interAssay_%s_%s.tab" % (specName, params['release'])
query = queries.activities(spec)
acts = queryDevice.queryDevice(query, params)
mkDict.activities(acts, dictFile)
writePairs.interAssaySampled(results, dictFile)
addProperties.addMolweight("molregno", results, params)
addProperties.addTargetClass("L1","accession", results, params)
addProperties.addSeq100(results)
if __name__ == '__main__':
import sys
if len(sys.argv) != 1: # the program name and the two arguments i
sys.exit("All parameters passed through gla.yaml")
interAssay()