diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rwxr-xr-x | wqflask/base/data_set.py | 71 |
1 files changed, 59 insertions, 12 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 96e04df0..9fa7beb3 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -168,13 +168,13 @@ class Markers(object): for marker, p_value in itertools.izip(self.markers, p_values): marker['p_value'] = p_value - if marker['p_value'] == 0: - marker['lod_score'] = 0 - marker['lrs_value'] = 0 - else: - marker['lod_score'] = -math.log10(marker['p_value']) - #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values - marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 + if math.isnan(marker['p_value']): + print("p_value is:", marker['p_value']) + marker['lod_score'] = -math.log10(marker['p_value']) + #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values + marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 + + class HumanMarkers(Markers): @@ -189,6 +189,8 @@ class HumanMarkers(Markers): marker['name'] = splat[1] marker['Mb'] = float(splat[3]) / 1000000 self.markers.append(marker) + + #print("markers is: ", pf(self.markers)) def add_pvalues(self, p_values): @@ -315,10 +317,10 @@ class DatasetGroup(object): #determine default genotype object if self.incparentsf1 and genotype_1.type != "intercross": - genotype = genotype_2 + self.genotype = genotype_2 else: self.incparentsf1 = 0 - genotype = genotype_1 + self.genotype = genotype_1 self.samplelist = list(genotype.prgy) @@ -436,8 +438,13 @@ class DataSet(object): print("Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass - def get_trait_data(self): - self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list + def get_trait_data(self, sample_list=None): + if sample_list: + self.samplelist = sample_list + self.group.parlist + self.group.f1list + else: + self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list + + query = """ SELECT Strain.Name, Strain.Id FROM Strain, Species WHERE Strain.Name IN {} @@ -1055,7 +1062,6 @@ class MrnaAssayDataSet(DataSet): """ % (escape(self.name), escape(self.dataset.name)) results = g.db.execute(query).fetchone() return results[0] - def retrieve_sample_data(self, trait): query = """ @@ -1076,6 +1082,47 @@ class MrnaAssayDataSet(DataSet): """ % (escape(trait), escape(self.name)) results = g.db.execute(query).fetchall() return results + + + def retrieve_genes(self, column_name): + query = """ + select ProbeSet.Name, ProbeSet.%s + from ProbeSet,ProbeSetXRef + where ProbeSetXRef.ProbeSetFreezeId = %s and + ProbeSetXRef.ProbeSetId=ProbeSet.Id; + """ % (column_name, escape(str(self.id))) + results = g.db.execute(query).fetchall() + + return dict(results) + + #def retrieve_gene_symbols(self): + # query = """ + # select ProbeSet.Name, ProbeSet.Symbol, ProbeSet.GeneId + # from ProbeSet,ProbeSetXRef + # where ProbeSetXRef.ProbeSetFreezeId = %s and + # ProbeSetXRef.ProbeSetId=ProbeSet.Id; + # """ % (self.id) + # results = g.db.execute(query).fetchall() + # symbol_dict = {} + # for item in results: + # symbol_dict[item[0]] = item[1] + # return symbol_dict + # + #def retrieve_gene_ids(self): + # query = """ + # select ProbeSet.Name, ProbeSet.GeneId + # from ProbeSet,ProbeSetXRef + # where ProbeSetXRef.ProbeSetFreezeId = %s and + # ProbeSetXRef.ProbeSetId=ProbeSet.Id; + # """ % (self.id) + # return process_and_run_query(query) + # results = g.db.execute(query).fetchall() + # symbol_dict = {} + # for item in results: + # symbol_dict[item[0]] = item[1] + # return symbol_dict + + class TempDataSet(DataSet): |