aboutsummaryrefslogtreecommitdiff
path: root/wqflask/base/trait.py
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask/base/trait.py')
-rwxr-xr-xwqflask/base/trait.py27
1 files changed, 22 insertions, 5 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 53f41779..f333d5a7 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,6 +1,8 @@
from __future__ import absolute_import, division, print_function
import string
+import resource
+
from htmlgen import HTMLgen2 as HT
@@ -15,6 +17,10 @@ from pprint import pformat as pf
from flask import Flask, g
+def print_mem(stage=""):
+ mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
+ print("{}: {}".format(stage, mem/1024))
+
class GeneralTrait(object):
"""
Trait class defines a trait in webqtl, can be either Microarray,
@@ -23,8 +29,12 @@ class GeneralTrait(object):
"""
def __init__(self, **kw):
- #print("in GeneralTrait")
- self.dataset = kw.get('dataset') # database name
+ # xor assertion
+ assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. xor name";
+ if kw.get('dataset_name'):
+ self.dataset = create_dataset(kw.get('dataset_name'))
+ else:
+ self.dataset = kw.get('dataset')
self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc.
self.cellid = kw.get('cellid')
self.identification = kw.get('identification', 'un-named trait')
@@ -39,8 +49,6 @@ class GeneralTrait(object):
# self.cellid is set to None above
elif len(name2) == 3:
self.dataset, self.name, self.cellid = name2
-
- self.dataset = create_dataset(self.dataset)
# Todo: These two lines are necessary most of the time, but perhaps not all of the time
# So we could add a simple if statement to short-circuit this if necessary
@@ -355,8 +363,17 @@ class GeneralTrait(object):
#traitQTL = self.cursor.fetchone()
if traitQTL:
self.locus, self.lrs, self.pvalue, self.mean = traitQTL
+ if self.locus:
+ result = g.db.execute("""
+ select Geno.Chr, Geno.Mb from Geno, Species
+ where Species.Name = '%s' and
+ Geno.Name = '%s' and
+ Geno.SpeciesId = Species.Id
+ """, (species, self.locus)).fetchone()
+ self.locus_chr = result[0]
+ self.locus_mb = result[1]
else:
- self.locus = self.lrs = self.pvalue = self.mean = ""
+ self.locus = self.locus_chr = self.locus_mb = self.lrs = self.pvalue = self.mean = ""
if self.dataset.type == 'Publish':
traitQTL = g.db.execute("""
SELECT