aboutsummaryrefslogtreecommitdiff
path: root/wqflask/base/trait.py
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask/base/trait.py')
-rwxr-xr-xwqflask/base/trait.py96
1 files changed, 61 insertions, 35 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 241bf2ab..82e013ae 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
@@ -15,22 +17,38 @@ from pprint import pformat as pf
from flask import Flask, g
-class GeneralTrait:
+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,
Published phenotype, genotype, or user input trait
"""
- def __init__(self, **kw):
- print("in GeneralTrait")
- self.dataset = kw.get('dataset') # database name
+ def __init__(self, get_qtl_info=False, **kw):
+ # 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')
self.haveinfo = kw.get('haveinfo', False)
self.sequence = kw.get('sequence') # Blat sequence, available for ProbeSet
self.data = kw.get('data', {})
+
+ # Sets defaultst
+ self.locus = None
+ self.lrs = None
+ self.pvalue = None
+ self.mean = None
+ self.num_overlap = None
+
if kw.get('fullname'):
name2 = value.split("::")
@@ -39,13 +57,12 @@ class GeneralTrait:
# 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
- self.retrieve_info()
+ self.retrieve_info(get_qtl_info=get_qtl_info)
self.retrieve_sample_data()
+
def get_name(self):
@@ -78,7 +95,7 @@ class GeneralTrait:
#desc = self.handle_pca(desc)
stringy = desc
return stringy
-
+
def display_name(self):
@@ -208,7 +225,7 @@ class GeneralTrait:
# ''' % (self.cellid, self.name, self.dataset.name)
#
#else:
- results = self.dataset.retrieve_sample_data(self)
+ results = self.dataset.retrieve_sample_data(self.name)
# Todo: is this necessary? If not remove
self.data.clear()
@@ -229,7 +246,7 @@ class GeneralTrait:
#def items(self):
# return self.__dict__.items()
- def retrieve_info(self, QTL=False):
+ def retrieve_info(self, get_qtl_info=False):
assert self.dataset, "Dataset doesn't exist"
if self.dataset.type == 'Publish':
query = """
@@ -269,7 +286,7 @@ class GeneralTrait:
escape(self.dataset.name),
escape(self.name))
traitInfo = g.db.execute(query).fetchone()
- print("traitInfo is: ", pf(traitInfo))
+ #print("traitInfo is: ", pf(traitInfo))
#XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
# to avoid the problem of same marker name from different species.
elif self.dataset.type == 'Geno':
@@ -287,7 +304,7 @@ class GeneralTrait:
escape(self.dataset.name),
escape(self.name))
traitInfo = g.db.execute(query).fetchone()
- print("traitInfo is: ", pf(traitInfo))
+ #print("traitInfo is: ", pf(traitInfo))
else: #Temp type
query = """SELECT %s FROM %s WHERE Name = %s
""" % (string.join(self.dataset.display_fields,','),
@@ -314,32 +331,32 @@ class GeneralTrait:
#XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number.
#XZ: So I have to test if geneid is number before execute the query.
#XZ: The geneid values in database should be cleaned up.
- try:
- junk = float(self.geneid)
- geneidIsNumber = 1
- except:
- geneidIsNumber = 0
-
- if geneidIsNumber:
- query = """
- SELECT
- HomologeneId
- FROM
- Homologene, Species, InbredSet
- WHERE
- Homologene.GeneId =%s AND
- InbredSet.Name = '%s' AND
- InbredSet.SpeciesId = Species.Id AND
- Species.TaxonomyId = Homologene.TaxonomyId
- """ % (escape(str(self.geneid)), escape(self.dataset.group.name))
- result = g.db.execute(query).fetchone()
- else:
- result = None
+ #try:
+ # float(self.geneid)
+ # geneidIsNumber = True
+ #except ValueError:
+ # geneidIsNumber = False
+
+ #if geneidIsNumber:
+ query = """
+ SELECT
+ HomologeneId
+ FROM
+ Homologene, Species, InbredSet
+ WHERE
+ Homologene.GeneId =%s AND
+ InbredSet.Name = '%s' AND
+ InbredSet.SpeciesId = Species.Id AND
+ Species.TaxonomyId = Homologene.TaxonomyId
+ """ % (escape(str(self.geneid)), escape(self.dataset.group.name))
+ result = g.db.execute(query).fetchone()
+ #else:
+ # result = None
if result:
self.homologeneid = result[0]
- if QTL:
+ if get_qtl_info:
if self.dataset.type == 'ProbeSet' and not self.cellid:
traitQTL = g.db.execute("""
SELECT
@@ -355,8 +372,17 @@ class GeneralTrait:
#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