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)
def orthologs():
import queryDevice
import mkDict
import queries
import writePairs
import os
import align
import addProperties
import mkHomologTable
import readIds
import yaml
# Read config file.
paramFile = open('gla.yaml')
params = yaml.safe_load(paramFile)
needlepath = params['needlepath']
vsCompara = params['vsCompara']
release = params['release']
comparaOrthologs = "data/orthologs_%s.txt"% params['vsCompara']
comparaHumanIds = "data/humanIds_%s.txt"% params['vsCompara']
comparaRatIds = "data/ratIds_%s.txt"% params['vsCompara']
# Assign output filenames.
dictFile = "data/ortho_compDict_%s.pkl"% params['release']
results = "data/orthologs_%s_%s.tab"%(params['release'], params['vsCompara'])
orthoTab = "data/orthologTable_%s.txt" % params['vsCompara']
# Create output files.
humanLkp = readIds.readIds(comparaHumanIds)
ratLkp = readIds.readIds(comparaRatIds)
mkHomologTable.homologTable(comparaOrthologs, orthoTab, humanLkp, ratLkp)
query = queries.paralogs(orthoTab)
acts= queryDevice.queryDevice(query, params)
mkDict.activities(acts, dictFile)
writePairs.homologMedian(params['homologyTypeOrthologs'], orthoTab, dictFile, results)
# Annotate output files.
align.pfam_a(results, params)
align.bSite(results, params)
addProperties.addMolweight('molregno', results, params)
addProperties.addTargetClass("L1","accession1", results, params)
addProperties.addPrefName("accession1", results, params)
addProperties.addPrefName("accession2", results, params)