Example #1
0
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)
Example #2
0
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)
Example #3
0
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)
Example #4
0
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)