def master(release, user, pword, host, port):
## Get all human protein coding genes from ensembl and a count of all uniqe domains.
import os
import pfamDomains #creates pfamDict and pfam_domains
import mapPfamDomains #Carry out the mapping and save results
import pdbChembl #Retrieves all binding site residues for interactions in ChEMBL.
import uniprotChembl ### Get all protein targets from ChEBML. ## Get Uniprot binding site annotation for each target.
import analysis #Carries out the analysis of the data generated in the previous steps.
import yaml #YAML is a data serialization format designed for human readability and interaction with scripting languages.
# Read config file.
paramFile = open('mpf.yaml')
params = yaml.safe_load(paramFile)
user = params['user']
pword = params['pword']
host = params['host']
port = params['port']
th = params['threshold']
# Get Uniprot identifiers for all human proteins.
os.system("R CMD BATCH --vanilla queryBioMaRt.R")
# Map Pfam domains and positions to all Uniprot identifiers.
#pfamDomains.pfamDomains(release, user, pword, host, port)
# Map small molecule binding to Pfam domains.
mapPfamDomains.mapPDs(th, release, user, pword, host, port)
def master(release, user, pword, host, port):
## Get all human protein coding genes from ensembl and a count of all uniqe domains.
import os
import pfamDomains
import mapPfamDomains
import pdbChembl
import uniprotChembl
import analysis
import yaml
# Read config file.
paramFile = open("mpf.yaml")
params = yaml.safe_load(paramFile)
user = params["user"]
pword = params["pword"]
host = params["host"]
port = params["port"]
th = params["threshold"]
# Get Uniprot identifiers for all human proteins.
os.system("R CMD BATCH --vanilla queryBioMaRt.R")
# Map Pfam domains and positions to all Uniprot identifiers.
# pfamDomains.pfamDomains(release, user, pword, host, port)
# Map small molecule binding to Pfam domains.
mapPfamDomains.mapPDs(th, release, user, pword, host, port)
def master(release, user, pword, host, port):
## Get all human protein coding genes from ensembl and a count of all uniqe domains.
import os
import pfamDomains
import mapPfamDomains
import pdbChembl
import uniprotChembl
import analysis
import yaml
# Read config file.
paramFile = open('mpf.yaml')
params = yaml.safe_load(paramFile)
user = params['user']
pword = params['pword']
host = params['host']
port = params['port']
th = params['threshold']
# Get Uniprot identifiers for all human proteins.
os.system("R CMD BATCH --vanilla queryBioMaRt.R")
# Map Pfam domains and positions to all Uniprot identifiers.
#pfamDomains.pfamDomains(release, user, pword, host, port)
# Map small molecule binding to Pfam domains.
mapPfamDomains.mapPDs(th, release, user, pword, host, port)
def master(release, user, pword, host, port):
## Get all human protein coding genes from ensembl and a count of all uniqe domains.
import os
import pfamDomains
import mapPfamDomains
import pdbChembl
import uniprotChembl
import analysis
#Set the threshold for ligand binding to 50 micromolar
th = 50
# Get Uniprot identifiers for all human proteins.
os.system("R CMD BATCH --vanilla queryBioMaRt.R")
# Map Pfam domains and positions to all Uniprot identifiers.
pfamDomains.pfamDomains(release, user, pword, host, port)
# Map small molecule binding to PFam domains.
mapPfamDomains.mapPDs(th, release, user, pword, host, port)
# Get all ChEMBL interactions in PDB and binding site residues.
pdbDict = pdbChembl.query(release, user, pword, host, port)
# Get all ChEMBL interactions in Uniprot and binding site annotation.
uniprotDict = uniprotChembl.query(release, user, pword, host, port)
# Analyze the data.
analysis.analysis(th, release, user, pword, host, port)