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-rwxr-xr-xwqflask/base/data_set.py85
-rwxr-xr-xwqflask/base/mrna_assay_tissue_data.py11
-rwxr-xr-xwqflask/base/trait.py4
3 files changed, 72 insertions, 28 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index f4ca3ae0..a2b13748 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -167,28 +167,56 @@ class Markers(object):
marker['Mb'] = float(marker['Mb'])
self.markers = markers
- print("self.markers:", self.markers)
+ #print("self.markers:", self.markers)
def add_pvalues(self, p_values):
print("length of self.markers:", len(self.markers))
print("length of p_values:", len(p_values))
- # THIS IS only needed for the case when we are limiting the number of p-values calculated
- if len(self.markers) < len(p_values):
- self.markers = self.markers[:len(p_values)]
-
- for marker, p_value in itertools.izip(self.markers, p_values):
- if not p_value:
- continue
- marker['p_value'] = float(p_value)
- if math.isnan(marker['p_value']) or 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 type(p_values) is list:
+ # THIS IS only needed for the case when we are limiting the number of p-values calculated
+ #if len(self.markers) > len(p_values):
+ # self.markers = self.markers[:len(p_values)]
+
+ for marker, p_value in itertools.izip(self.markers, p_values):
+ if not p_value:
+ continue
+ marker['p_value'] = float(p_value)
+ if math.isnan(marker['p_value']) or 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
+ elif type(p_values) is dict:
+ filtered_markers = []
+ for marker in self.markers:
+ #print("marker[name]", marker['name'])
+ #print("p_values:", p_values)
+ if marker['name'] in p_values:
+ #print("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
+ 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
+ filtered_markers.append(marker)
+ #else:
+ #print("marker {} NOT in p_values".format(i))
+ #self.markers.remove(marker)
+ #del self.markers[i]
+ self.markers = filtered_markers
+
+ #for i, marker in enumerate(self.markers):
+ # if not 'p_value' in marker:
+ # #print("self.markers[i]", self.markers[i])
+ # del self.markers[i]
+ # #self.markers.remove(self.markers[i])
class HumanMarkers(Markers):
@@ -226,15 +254,15 @@ class HumanMarkers(Markers):
# #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
- print("p_values2:", p_values)
+ #print("p_values2:", pf(p_values))
super(HumanMarkers, self).add_pvalues(p_values)
- with Bench("deleting markers"):
- markers = []
- for marker in self.markers:
- if not marker['Mb'] <= 0 and not marker['chr'] == 0:
- markers.append(marker)
- self.markers = markers
+ #with Bench("deleting markers"):
+ # markers = []
+ # for marker in self.markers:
+ # if not marker['Mb'] <= 0 and not marker['chr'] == 0:
+ # markers.append(marker)
+ # self.markers = markers
@@ -254,7 +282,7 @@ class DatasetGroup(object):
self.name = "BXD"
self.f1list = None
- self.parlist = None
+ self.parlist = None
self.get_f1_parent_strains()
#print("parents/f1s: {}:{}".format(self.parlist, self.f1list))
@@ -476,8 +504,9 @@ class DataSet(object):
else:
self.samplelist = self.group.samplelist
- if (self.group.parlist + self.group.f1list) in self.samplelist:
- self.samplelist += self.group.parlist + self.group.f1list
+ 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
@@ -547,7 +576,11 @@ class DataSet(object):
order by {}.Id
""".format(*mescape(self.type, self.type, self.type, self.type,
self.name, dataset_type, self.type, self.type, dataset_type))
+
+ #print("trait data query: ", query)
+
results = g.db.execute(query).fetchall()
+ #print("query results:", results)
trait_sample_data.append(results)
trait_count = len(trait_sample_data[0])
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index be5df657..1a05fce7 100755
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -19,6 +19,8 @@ class MrnaAssayTissueData(object):
if self.gene_symbols == None:
self.gene_symbols = []
+ print("self.gene_symbols:", self.gene_symbols)
+
self.data = collections.defaultdict(Bunch)
#self.gene_id_dict ={}
@@ -28,7 +30,7 @@ class MrnaAssayTissueData(object):
#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
+ 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
from TissueProbeSetXRef
@@ -53,6 +55,7 @@ class MrnaAssayTissueData(object):
'''.format(in_clause)
results = g.db.execute(query).fetchall()
+
for result in results:
symbol = result[0]
if symbol in gene_symbols:
@@ -66,7 +69,7 @@ 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))
+ print("self.data: ", pf(self.data))
###########################################################################
#Input: cursor, symbolList (list), dataIdDict(Dict)
@@ -79,6 +82,8 @@ class MrnaAssayTissueData(object):
def get_symbol_values_pairs(self):
id_list = [self.data[symbol].data_id for symbol in self.data]
+ print("id_list:", id_list)
+
symbol_values_dict = {}
query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value
@@ -86,6 +91,8 @@ class MrnaAssayTissueData(object):
WHERE TissueProbeSetData.Id IN {} and
TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
+ print("TISSUE QUERY:", query)
+
results = g.db.execute(query).fetchall()
for result in results:
if result.Symbol.lower() not in symbol_values_dict:
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 712d9af5..3f80d4a4 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -40,6 +40,7 @@ class GeneralTrait(object):
else:
self.dataset = kw.get('dataset')
self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc.
+ print("THE NAME IS:", self.name)
self.cellid = kw.get('cellid')
self.identification = kw.get('identification', 'un-named trait')
self.haveinfo = kw.get('haveinfo', False)
@@ -295,6 +296,9 @@ class GeneralTrait(object):
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishFreeze.Id = %s
""" % (self.name, self.dataset.id)
+
+ print("query is:", query)
+
trait_info = g.db.execute(query).fetchone()
#XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
#XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.