def init(filename, __EXCLUDE_PSEUDOGENES=0):
global __geneDB, __symbols, __gene_symbol_parents, __gene_symbol_synonyms
__geneDB = pyCSV()
__geneDB.load(filename,"\t")
for row in xrange(1, __geneDB.rows+1):
if __EXCLUDE_PSEUDOGENES and __geneDB.get(row, 2).count("pseudogene")>0:
continue
symbol = geneUtils.formatGeneSymbol(__geneDB.get(row, 1))
__original_names[symbol] = __geneDB.get(row, 1)
__symbols.add(symbol)
__sym_rows[symbol] = row
if __isApproved(symbol):
__approved_symbols.add(symbol)
print "Loaded:", len(__approved_symbols), "approved gene symbols..."
for symbol in __approved_symbols:
past_symbols = getPastSymbols(symbol)
for child in past_symbols:
try:
__gene_symbol_parents[child].add(symbol)
except KeyError:
__gene_symbol_parents[child] = set([symbol])
for synSym in getSynonyms(symbol):
try:
__gene_symbol_synonyms[synSym].add(symbol)
except KeyError:
__gene_symbol_synonyms[synSym] = set([symbol])
for symbol in __gene_symbol_synonyms:
remove = []
for synGene in __gene_symbol_synonyms[symbol]:
if synGene not in __approved_symbols:
remove.append(synGene)
for r in remove:
__gene_symbol_synonyms[symbol].remove(r)
def loadEvolutionaryGenes(filename, __ENABLE_GENE_VERIFICATION=0,
__ENABLE_GENE_UPDATES=0, __CROSS_MATCH_LEVEL = 1, include_studies = [1,2,3,4,5]):
global __DEBUG
genesTSV = pyCSV()
genesTSV.load(filename, "\t")
bustamante = []
vamathevan_human = []
kosiol_human = []
if 1 in include_studies:
bustamante = [item.lower() for item in geneUtils.columnToList(genesTSV, 1, 2)]
if 2 in include_studies:
vamathevan_human = [item.lower() for item in geneUtils.columnToList(genesTSV, 3, 2)]
if 3 in include_studies:
kosiol_human = [item.lower() for item in geneUtils.columnToList(genesTSV, 8, 2)]
conflicts = []
bakewell = []
nielsen = []
if 4 in include_studies:
bakewell, c = geneUtils.mergeColumns(genesTSV, 12, 13, 2)
bakewell = [item.lower() for item in bakewell]
conflicts.extend(c)
if 5 in include_studies:
nielsen, c = geneUtils.mergeColumns(genesTSV, 17, 18, 2)
nielsen = [item.lower() for item in nielsen]
conflicts.extend(c)
# verify gene symbols
duplicates = 0
geneCounts = {}
geneUtils.geneFrequency(geneCounts, bustamante)
geneUtils.geneFrequency(geneCounts, vamathevan_human)
geneUtils.geneFrequency(geneCounts, kosiol_human)
geneUtils.geneFrequency(geneCounts, bakewell)
geneUtils.geneFrequency(geneCounts, nielsen)
#duplicates+=geneUtils.addAll(geneSet, bustamante)
#duplicates+=geneUtils.addAll(geneSet, vamathevan_human)
#duplicates+=geneUtils.addAll(geneSet, kosiol_human)
#duplicates+=geneUtils.addAll(geneSet, bakewell)
#duplicates+=geneUtils.addAll(geneSet, nielsen)
if __ENABLE_GENE_VERIFICATION:
for pair in conflicts:
g1 = pair[0].lower()
g2 = pair[1].lower()
if __ENABLE_GENE_UPDATES:
g1parent = geneDB.findUpdatedSymbol(g1)
g2parent = geneDB.findUpdatedSymbol(g2)
if g1parent != None:
g1 = g1parent
if g2parent != None:
g2 = g2parent
if geneDB.isApproved(g1):
if __DEBUG>1:
print "Gene", g2, "not approved, but",g1,"is fine"
try:
geneCounts[g1]+=1
except KeyError:
geneCounts[g1] = 1
elif geneDB.isApproved(g2):
if __DEBUG>1:
print "Gene", g1, "not approved, but",g2,"is fine"
try:
geneCounts[g2]+=1
except KeyError:
geneCounts[g2] = 1
else:
if __DEBUG>1:
print "Neither",g1,"nor",g2,"are valid"
else:
for pair in conflicts:
g1 = pair[0].lower()
g2 = pair[1].lower()
try:
geneCounts[g2]+=1
except KeyError:
geneCounts[g2] = 1
duplicates, geneSet = geneUtils.addFilterFrequency(geneCounts, __CROSS_MATCH_LEVEL)
ofile = open(os.sep.join(["results","log","geneSetDuplicateFrequency.txt"]),'w')
glist = []
for gene in geneCounts:
glist.append((gene, geneCounts[gene]))
for item in sorted(glist, key=lambda item: -item[1]):
ofile.write("%-20s%d\n" % item)
ofile.close()
geneSet = set([geneUtils.formatGeneSymbol(geneSym) for geneSym in geneSet])
if __ENABLE_GENE_UPDATES:
geneUtils.updateGeneSet(geneSet)
if __ENABLE_GENE_VERIFICATION:
geneUtils.removeInvalidGenes(geneSet)
if __DEBUG>0:
print "\n-----------------------------"
print "Total Duplicates: ", duplicates
print "Total Name Conflicts: ", len(conflicts)
print "Total Genes Remaining: ", len(geneSet)
print "-----------------------------\n"
log_file = open(os.sep.join(["results","log","loaded_genelist.txt"]),'w')
for gene in geneSet:
log_file.write(gene+"\n")
log_file.close()
return geneSet
from pyCSV import *
import geneUtils
import geneVerifier as geneDB
import os
__DEBUG=0
__geneSet = set([])
__traitDict = {}
__studyByGene = {}
__studyByTrait = {}
__pValues = {}
__studyGenes = {}
__gwasCatalogue = pyCSV()
def getTraitsForGene(geneSym):
if geneSym in __traitDict:
return __traitDict[geneSym]
return set([])
def getDavidBackgroundSet(pvalue = 0.05):
geneList = set([])
for studyId in __studyGenes:
if __pValues[studyId] < pvalue:
for geneSym in __studyGenes[studyId]:
geneList.add(geneSym)
return geneList
def getGenesForTrait(trait, pvalue = 0.05):
geneList = set([])
for studyId in __studyByTrait[trait]:
import geneVerifier as geneDB
from pyFASTA import *
from geneUtils import *
from pyCSV import *
import geneUtils
import os
__DEBUG = 1
__targetCatalogue = pyCSV()
__drugCatalogue = pyCSV()
__geneSet = set([])
__geneNames = {}
__drugDict = {}
__drugs = {}
def getDrugsTargetingProteinSet(proteins):
drugSet = set([])
for protein in proteins:
if protein in __drugDict:
drugSet |= __drugDict[protein]
return drugSet
def initDruglist(drug_file):
global __DEBUG
__drugCatalogue.load(drug_file)
for r in xrange(1, __drugCatalogue.rows+1):
db_id = __drugCatalogue.get(r, 0)
