def gene_symb_to_probe_id(symbol_list):
'''
-given a list of gene symbols, return affy U133A probe ids
'''
mc = mu.MongoContainer()
# geneInfo = mc.gene_info.find({'pr_id':{'$in':list(probe_matrix.index.values)}},
# {'pr_id':True,'pr_gene_symbol':True},toDataFrame=True)
geneInfo = mc.gene_info.find({'pr_gene_symbol':{'$in':symbol_list}},
{'pr_id':True,'pr_gene_symbol':True},toDataFrame=True)
geneInfo = geneInfo[~geneInfo.pr_id.isnull()]
probe_list = list(geneInfo.pr_id.values)
return probe_list
def get_dos_BRDs():
'return Series of all DOS compounds - use the DOS icollection'
#get all cps from DOS collection
mc = mu.MongoContainer()
pertInfo = mc.pert_info.find({'pert_icollection':'DOS'},
{},toDataFrame=True)
#check that it doesn't have a known pert_iname
inameSer = pertInfo['pert_iname']
inameFrm = pd.DataFrame(inameSer)
#which values do not start with BRD?
notBRDiname = pertInfo[~inameSer.str.contains('BRD')]
isBRDiname = pertInfo[inameSer.str.contains('BRD')]
dosBrds = isBRDiname['pert_id']
return dosBrds
def probe_id_to_gene_symb(inFile, outFile):
'''
-change the first column of probe_ids in a gct to gene symbols
'''
mtrx = pd.read_csv(inFile, sep='\t', skiprows=[0, 1],
index_col=0) #,header=True
probe_ids = mtrx.index.values
mc = mu.MongoContainer()
geneInfo = mc.gene_info.find({'pr_id': {
'$in': list(probe_ids)
}}, {
'pr_id': True,
'pr_gene_symbol': True
},
toDataFrame=True)
geneInfo.index = geneInfo.pr_id
geneInfo = geneInfo.reindex(mtrx.index.values)
mtrx.index = geneInfo.pr_gene_symbol.values
mtrx.index.name = 'Name'
mtrx.to_csv(outFile, sep='\t')
line_pre_adder(outFile, str(mtrx.shape[0]) + '\t' + str(mtrx.shape[1] - 1))
line_pre_adder(outFile, "#1.2")
##grab anything that appeared on a DOS plate
# CM = mu.CMapMongo()
# dosQuery = CM.find({'sig_id':{'$regex':'DOS'},'pert_type':'trt_cp'}, #,
# {'sig_id':True,'pert_id':True,'cell_id':True,'pert_time':True,'is_gold':True,'pert_iname':True,'distil_ss':True,'distil_cc_q75':True},
# toDataFrame=True)
# potentialDos = set(dosQuery['pert_id'])
# #check the pert_collection status of each compounds
# mc = mu.MongoContainer()
# pertInfo = mc.pert_info.find({'pert_id':{'$in':list(potentialDos)}},
# {},toDataFrame=True)
# collectionSets = set(pertInfo['pert_icollection'])
#get all cps from DOS collection
mc = mu.MongoContainer()
pertInfo = mc.pert_info.find({'pert_icollection':'DOS'},
{},toDataFrame=True)
#check that it doesn't have a known pert_iname
inameSer = pertInfo['pert_iname']
inameFrm = pd.DataFrame(inameSer)
#which values do not start with BRD?
notBRDiname = pertInfo[~inameSer.str.contains('BRD')]
isBRDiname = pertInfo[inameSer.str.contains('BRD')]
dosBrds = isBRDiname['pert_id']
########################
## all DOS signatures ##
########################
# get signatures for all DOS compounds
