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-rwxr-xr-xwqflask/base/data_set.py123
-rwxr-xr-xwqflask/base/trait.py4
2 files changed, 70 insertions, 57 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index c2380f8c..4c5c46a5 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -672,12 +672,13 @@ class MrnaAssayDataSet(DataSet):
query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(self.type,
self.type,
self.type))
- #XZ, 03/04/2009: Xiaodong changed Data to %sData and changed parameters from %(item,item, db.type,item,item) to %(db.type, item,item, db.type,item,item)
+
for item in sample_ids_step:
query += """
left join {}Data as T{} on T{}.Id = {}XRef.DataId
and T{}.StrainId={}\n
""".format(*mescape(self.type, item, item, self.type, item, item))
+
query += """
WHERE {}XRef.{}FreezeId = {}Freeze.Id
and {}Freeze.Name = '{}'
@@ -690,17 +691,19 @@ class MrnaAssayDataSet(DataSet):
trait_count = len(trait_sample_data[0])
self.trait_data = collections.defaultdict(list)
+
# put all of the separate data together into a dictionary where the keys are
# trait names and values are lists of sample values
- for j in range(trait_count):
- trait_name = trait_sample_data[0][j][0]
- for i in range(int(number_chunks)):
- self.trait_data[trait_name] += trait_sample_data[i][j][data_start_pos:]
-
+ for trait_counter in range(trait_count):
+ trait_name = trait_sample_data[0][trait_counter][0]
+ for chunk_counter in range(int(number_chunks)):
+ self.trait_data[trait_name] += (
+ trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
+
def get_trait_info(self, trait_list=None, species=''):
- # Note: setting trait_list to [] is probably not a great idea.
+ # Note: setting trait_list to [] is probably not a great idea.
if not trait_list:
trait_list = []
@@ -709,9 +712,7 @@ class MrnaAssayDataSet(DataSet):
if not this_trait.haveinfo:
this_trait.retrieveInfo(QTL=1)
- if this_trait.symbol:
- pass
- else:
+ if not this_trait.symbol:
this_trait.symbol = "N/A"
#XZ, 12/08/2008: description
@@ -719,60 +720,56 @@ class MrnaAssayDataSet(DataSet):
description_string = str(this_trait.description).strip()
target_string = str(this_trait.probe_target_description).strip()
- description_display = ''
-
if len(description_string) > 1 and description_string != 'None':
description_display = description_string
else:
description_display = this_trait.symbol
- if len(description_display) > 1 and description_display != 'N/A' and len(target_string) > 1 and target_string != 'None':
+ if (len(description_display) > 1 and description_display != 'N/A' and
+ len(target_string) > 1 and target_string != 'None'):
description_display = description_display + '; ' + target_string.strip()
# Save it for the jinja2 template
this_trait.description_display = description_display
- #print(" xxxxdd [%s]: %s" % (type(this_trait.description_display), description_display))
#XZ: trait_location_value is used for sorting
trait_location_repr = 'N/A'
trait_location_value = 1000000
if this_trait.chr and this_trait.mb:
- try:
- trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
- except:
- if this_trait.chr.upper() == 'X':
- trait_location_value = 20*1000 + this_trait.mb
- else:
- trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb
-
- this_trait.location_repr = 'Chr %s: %.4f Mb' % (this_trait.chr, float(this_trait.mb) )
+ #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
+ #This is so we can convert the location to a number used for sorting
+ trait_location_value = self.convert_location_to_value(this_trait.chr, this_trait.mb)
+ #try:
+ # trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
+ #except ValueError:
+ # if this_trait.chr.upper() == 'X':
+ # trait_location_value = 20*1000 + this_trait.mb
+ # else:
+ # trait_location_value = (ord(str(this_trait.chr).upper()[0])*1000 +
+ # this_trait.mb)
+
+ #ZS: Put this in function currently called "convert_location_to_value"
+ this_trait.location_repr = 'Chr %s: %.4f Mb' % (this_trait.chr,
+ float(this_trait.mb))
this_trait.location_value = trait_location_value
- #this_trait.trait_location_value = trait_location_value
- #XZ, 01/12/08: This SQL query is much faster.
+ #Get mean expression value
query = (
-"""select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
- where ProbeSetXRef.ProbeSetFreezeId = %s and
- ProbeSet.Id = ProbeSetXRef.ProbeSetId and
- ProbeSet.Name = '%s'
+ """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
+ where ProbeSetXRef.ProbeSetFreezeId = %s and
+ ProbeSet.Id = ProbeSetXRef.ProbeSetId and
+ ProbeSet.Name = '%s'
""" % (escape(str(this_trait.dataset.id)),
escape(this_trait.name)))
print("query is:", pf(query))
result = g.db.execute(query).fetchone()
+
+ mean = result[0] if result else 0
- if result:
- if result[0]:
- mean = result[0]
- else:
- mean=0
- else:
- mean = 0
-
- #XZ, 06/05/2009: It is neccessary to turn on nowrap
- this_trait.mean = repr = "%2.3f" % mean
+ this_trait.mean = "%2.3f" % mean
#LRS and its location
this_trait.LRS_score_repr = 'N/A'
@@ -791,23 +788,39 @@ class MrnaAssayDataSet(DataSet):
result = self.cursor.fetchone()
if result:
- if result[0] and result[1]:
- LRS_Chr = result[0]
- LRS_Mb = result[1]
-
- #XZ: LRS_location_value is used for sorting
- try:
- LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb)
- except:
- if LRS_Chr.upper() == 'X':
- LRS_location_value = 20*1000 + float(LRS_Mb)
- else:
- LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb)
+ #if result[0] and result[1]:
+ # lrs_chr = result[0]
+ # lrs_mb = result[1]
+ lrs_chr, lrs_mb = result
+ #XZ: LRS_location_value is used for sorting
+ lrs_location_value = self.convert_location_to_value(lrs_chr, lrs_mb)
+
+ #try:
+ # lrs_location_value = int(lrs_chr)*1000 + float(lrs_mb)
+ #except:
+ # if lrs_chr.upper() == 'X':
+ # lrs_location_value = 20*1000 + float(lrs_mb)
+ # else:
+ # lrs_location_value = (ord(str(LRS_chr).upper()[0])*1000 +
+ # float(lrs_mb))
+
+ this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
+ this_trait.LRS_score_value = this_trait.lrs
+ this_trait.LRS_location_repr = 'Chr %s: %.4f Mb' % (lrs_chr, float(lrs_mb))
+
+
+ def convert_location_to_value(chromosome, mb):
+ try:
+ location_value = int(chromosome)*1000 + float(mb)
+ except ValueError:
+ if chromosome.upper() == 'X':
+ location_value = 20*1000 + float(mb)
+ else:
+ location_value = (ord(str(chromosome).upper()[0])*1000 +
+ float(mb))
+
+ return location_value
- this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
- this_trait.LRS_score_value = LRS_score_value = this_trait.lrs
- this_trait.LRS_location_repr = LRS_location_repr = 'Chr %s: %.4f Mb' % (LRS_Chr, float(LRS_Mb) )
-
def get_sequence(self):
query = """
SELECT
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7c1c035c..5fde114f 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -15,7 +15,7 @@ from pprint import pformat as pf
from flask import Flask, g
-class GeneralTrait:
+class GeneralTrait(object):
"""
Trait class defines a trait in webqtl, can be either Microarray,
Published phenotype, genotype, or user input trait
@@ -78,7 +78,7 @@ class GeneralTrait:
#desc = self.handle_pca(desc)
stringy = desc
return stringy
-
+
def display_name(self):