diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 37 |
1 files changed, 0 insertions, 37 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 468c4da0..d0f5e6f2 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -655,42 +655,7 @@ class DataSet(object): "Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass - def fetch_probe_trait_data(self, sample_list=None): - if sample_list: - self.samplelist = sample_list - else: - self.samplelist = self.group.samplelist - - if self.group.parlist != None and self.group.f1list != None: - if (self.group.parlist + self.group.f1list) in self.samplelist: - self.samplelist += self.group.parlist + self.group.f1list - - query = """ - SELECT Strain.Name, Strain.Id FROM Strain, Species - WHERE Strain.Name IN {} - and Strain.SpeciesId=Species.Id - and Species.name = '{}' - """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) - logger.sql(query) - results = dict(g.db.execute(query).fetchall()) - sample_ids = [results[item] for item in self.samplelist] - - query = """SELECT * from ProbeSetData WHERE Id in ( SELECT ProbeSetXRef.DataId FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze) WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and ProbeSetFreeze.Name = 'HC_M2_0606_P' and ProbeSet.Id = ProbeSetXRef.ProbeSetId order by ProbeSet.Id ) and StrainId in ({})""".format( - ",".join(str(sample_id) for sample_id in sample_ids)) - results = g.db.execute(query).fetchall() - - # with conn: - # cursor = conn.cursor() - # cursor.execute(query) - # results = cursor.fetchall() - trait_data = {} - for trait_id, StrainId, value in results: - if trait_id in trait_data: - trait_data[trait_id].append(value) - else: - trait_data[trait_id] = [value] - self.trait_data = trait_data def get_trait_data(self, sample_list=None): if sample_list: @@ -711,7 +676,6 @@ class DataSet(object): logger.sql(query) results = dict(g.db.execute(query).fetchall()) sample_ids = [results[item] for item in self.samplelist] - print("the number of sample ids are", len(sample_ids)) # MySQL limits the number of tables that can be used in a join to 61, # so we break the sample ids into smaller chunks @@ -762,7 +726,6 @@ class DataSet(object): trait_sample_data.append(results) trait_count = len(trait_sample_data[0]) - print("the trait count is >>>", trait_count) self.trait_data = collections.defaultdict(list) # put all of the separate data together into a dictionary where the keys are |