From f4fbb6d53419a19c6ee67977d18605cdcbb09c0e Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 12 Aug 2021 22:35:53 +0000 Subject: add function for reading in JSON file that lists sample lists unique to each study within a group (in this case only BXD Longevity for now) --- wqflask/base/data_set.py | 9 +++++++++ 1 file changed, 9 insertions(+) (limited to 'wqflask/base/data_set.py') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 4cb82665..b8f2f9fb 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -398,6 +398,15 @@ class DatasetGroup: if maternal and paternal: self.parlist = [maternal, paternal] + def get_study_samplelists(self): + study_sample_file = "%s/study_sample_lists/%s.json" % (webqtlConfig.GENODIR, self.name) + try: + f = open(study_sample_file) + except: + return None + study_samples = json.load(f) + return study_samples + def get_genofiles(self): jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name) try: -- cgit v1.2.3 From 98683bd5cc809aa03e0bd58a67733498b4f56a9d Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 12 Aug 2021 23:17:04 +0000 Subject: Fix the way the study_sample_lists path is set and checked --- wqflask/base/data_set.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask/base/data_set.py') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index b8f2f9fb..1042e1bd 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -399,7 +399,7 @@ class DatasetGroup: self.parlist = [maternal, paternal] def get_study_samplelists(self): - study_sample_file = "%s/study_sample_lists/%s.json" % (webqtlConfig.GENODIR, self.name) + study_sample_file = locate_ignore_error(self.name + ".json", 'study_sample_lists') try: f = open(study_sample_file) except: -- cgit v1.2.3 From 810b2ace0a9cb2511cf0ef6f0c01f70a0ce11915 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 12 Aug 2021 23:19:38 +0000 Subject: Return empty list instead of None in get_study_samplelists --- wqflask/base/data_set.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask/base/data_set.py') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 1042e1bd..0ea61faa 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -403,7 +403,7 @@ class DatasetGroup: try: f = open(study_sample_file) except: - return None + return [] study_samples = json.load(f) return study_samples -- cgit v1.2.3 From 579ae94b08f0b1cef00350b54dadc12869ad70de Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 6 Aug 2021 16:15:17 +0300 Subject: base: data_set: Remove unnecessary comments and logging statements --- wqflask/base/data_set.py | 12 ------------ 1 file changed, 12 deletions(-) (limited to 'wqflask/base/data_set.py') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 4cb82665..edc22540 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -277,7 +277,6 @@ class Markers: filtered_markers = [] for marker in self.markers: if marker['name'] in p_values: - # logger.debug("marker {} IS in p_values".format(i)) marker['p_value'] = p_values[marker['name']] if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 @@ -298,7 +297,6 @@ class HumanMarkers(Markers): self.markers = [] for line in marker_data_fh: splat = line.strip().split() - # logger.debug("splat:", splat) if len(specified_markers) > 0: if splat[1] in specified_markers: marker = {} @@ -737,7 +735,6 @@ class DataSet: 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] @@ -908,7 +905,6 @@ class PhenotypeDataSet(DataSet): Geno.Name = '%s' and Geno.SpeciesId = Species.Id """ % (species, this_trait.locus) - logger.sql(query) result = g.db.execute(query).fetchone() if result: @@ -938,7 +934,6 @@ class PhenotypeDataSet(DataSet): Order BY Strain.Name """ - logger.sql(query) results = g.db.execute(query, (trait, self.id)).fetchall() return results @@ -1005,7 +1000,6 @@ class GenotypeDataSet(DataSet): Order BY Strain.Name """ - logger.sql(query) results = g.db.execute(query, (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name)).fetchall() @@ -1126,8 +1120,6 @@ class MrnaAssayDataSet(DataSet): ProbeSet.Name = '%s' """ % (escape(str(this_trait.dataset.id)), escape(this_trait.name))) - - logger.sql(query) result = g.db.execute(query).fetchone() mean = result[0] if result else 0 @@ -1147,7 +1139,6 @@ class MrnaAssayDataSet(DataSet): Geno.Name = '{}' and Geno.SpeciesId = Species.Id """.format(species, this_trait.locus) - logger.sql(query) result = g.db.execute(query).fetchone() if result: @@ -1179,7 +1170,6 @@ class MrnaAssayDataSet(DataSet): Order BY Strain.Name """ % (escape(trait), escape(self.name)) - logger.sql(query) results = g.db.execute(query).fetchall() return results @@ -1190,7 +1180,6 @@ class MrnaAssayDataSet(DataSet): where ProbeSetXRef.ProbeSetFreezeId = %s and ProbeSetXRef.ProbeSetId=ProbeSet.Id; """ % (column_name, escape(str(self.id))) - logger.sql(query) results = g.db.execute(query).fetchall() return dict(results) @@ -1224,7 +1213,6 @@ def geno_mrna_confidentiality(ob): query = '''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name) - logger.sql(query) result = g.db.execute(query) (dataset_id, -- cgit v1.2.3