diff options
Diffstat (limited to 'wqflask/base/mrna_assay_tissue_data.py')
| -rw-r--r-- | wqflask/base/mrna_assay_tissue_data.py | 66 |
1 files changed, 1 insertions, 65 deletions
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index eb836e6c..6fec5dcd 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -18,21 +18,11 @@ class MrnaAssayTissueData(object): def __init__(self, gene_symbols=None): self.gene_symbols = gene_symbols - self.have_data = False if self.gene_symbols == None: self.gene_symbols = [] - #print("self.gene_symbols:", self.gene_symbols) - self.data = collections.defaultdict(Bunch) - #self.gene_id_dict ={} - #self.data_id_dict = {} - #self.chr_dict = {} - #self.mb_dict = {} - #self.desc_dict = {} - #self.probe_target_desc_dict = {} - query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description from ( select Symbol, max(Mean) as maxmean @@ -52,7 +42,6 @@ class MrnaAssayTissueData(object): in_clause = db_tools.create_in_clause(gene_symbols) #ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower - query += ''' Symbol in {} group by Symbol) as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol and t.Mean = x.maxmean; @@ -67,9 +56,7 @@ class MrnaAssayTissueData(object): for result in results: symbol = result[0] - #if symbol.lower() in [gene_symbol.lower() for gene_symbol in gene_symbols]: if symbol.lower() in lower_symbols: - #gene_symbols.append(symbol) symbol = symbol.lower() self.data[symbol].gene_id = result.GeneId @@ -79,8 +66,6 @@ class MrnaAssayTissueData(object): self.data[symbol].description = result.description self.data[symbol].probe_target_description = result.Probe_Target_Description - print("self.data: ", pf(self.data)) - ########################################################################### #Input: cursor, symbolList (list), dataIdDict(Dict) #output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair, @@ -107,53 +92,4 @@ class MrnaAssayTissueData(object): else: symbol_values_dict[result.Symbol.lower()].append(result.value) - #for symbol in self.data: - # data_id = self.data[symbol].data_id - # symbol_values_dict[symbol] = self.get_tissue_values(data_id) - - - return symbol_values_dict - - - #def get_tissue_values(self, data_id): - # """Gets the tissue values for a particular gene""" - # - # tissue_values=[] - # - # query = """SELECT value, id - # FROM TissueProbeSetData - # WHERE Id IN {}""".format(db_tools.create_in_clause(data_id)) - # - # #try : - # results = g.db.execute(query).fetchall() - # for result in results: - # tissue_values.append(result.value) - # #symbol_values_dict[symbol] = value_list - # #except: - # # symbol_values_pairs[symbol] = None - # - # return tissue_values - -######################################################################################################## -#input: cursor, symbolList (list), dataIdDict(Dict): key is symbol -#output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair. -# key is symbol, value is one list of expression values of one probeSet. -#function: wrapper function for getSymbolValuePairDict function -# build gene symbol list if necessary, cut it into small lists if necessary, -# then call getSymbolValuePairDict function and merge the results. -######################################################################################################## - -#def get_trait_symbol_and_tissue_values(symbol_list=None): -# tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list) -# -# #symbolList, -# #geneIdDict, -# #dataIdDict, -# #ChrDict, -# #MbDict, -# #descDict, -# #pTargetDescDict = getTissueProbeSetXRefInfo( -# # GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId) -# -# if len(tissue_data.gene_symbols): -# return get_symbol_values_pairs(tissue_data) + return symbol_values_dict
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