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-rwxr-xr-xwqflask/base/trait.py101
1 files changed, 70 insertions, 31 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index dde8b8d8..db76ddea 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. or 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):
@@ -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 = """
@@ -251,7 +268,7 @@ class GeneralTrait:
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishFreeze.Id = %s
""" % (self.name, self.dataset.id)
- traitInfo = g.db.execute(query).fetchone()
+ 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.
elif self.dataset.type == 'ProbeSet':
@@ -268,8 +285,8 @@ class GeneralTrait:
""" % (escape(display_fields_string),
escape(self.dataset.name),
escape(self.name))
- traitInfo = g.db.execute(query).fetchone()
- print("traitInfo is: ", pf(traitInfo))
+ trait_info = g.db.execute(query).fetchone()
+ #print("trait_info is: ", pf(trait_info))
#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':
@@ -286,23 +303,24 @@ class GeneralTrait:
""" % (escape(display_fields_string),
escape(self.dataset.name),
escape(self.name))
- traitInfo = g.db.execute(query).fetchone()
- print("traitInfo is: ", pf(traitInfo))
+ trait_info = g.db.execute(query).fetchone()
+ #print("trait_info is: ", pf(trait_info))
else: #Temp type
query = """SELECT %s FROM %s WHERE Name = %s
""" % (string.join(self.dataset.display_fields,','),
self.dataset.type, self.name)
- traitInfo = g.db.execute(query).fetchone()
+ trait_info = g.db.execute(query).fetchone()
#self.cursor.execute(query)
- #traitInfo = self.cursor.fetchone()
- if traitInfo:
+ #trait_info = self.cursor.fetchone()
+ if trait_info:
self.haveinfo = True
#XZ: assign SQL query result to trait attributes.
for i, field in enumerate(self.dataset.display_fields):
- setattr(self, field, str(traitInfo[i]))
+ print(" mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i]))
+ setattr(self, field, trait_info[i])
if self.dataset.type == 'Publish':
self.confidential = 0
@@ -310,6 +328,10 @@ class GeneralTrait:
self.confidential = 1
self.homologeneid = None
+
+ print("self.geneid is:", self.geneid)
+ print(" type:", type(self.geneid))
+ print("self.dataset.group.name is:", self.dataset.group.name)
if self.dataset.type == 'ProbeSet' and self.dataset.group and self.geneid:
#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.
@@ -321,6 +343,8 @@ class GeneralTrait:
# geneidIsNumber = False
#if geneidIsNumber:
+
+
query = """
SELECT
HomologeneId
@@ -332,6 +356,7 @@ class GeneralTrait:
InbredSet.SpeciesId = Species.Id AND
Species.TaxonomyId = Homologene.TaxonomyId
""" % (escape(str(self.geneid)), escape(self.dataset.group.name))
+ print("-> query is:", query)
result = g.db.execute(query).fetchone()
#else:
# result = None
@@ -339,26 +364,40 @@ class GeneralTrait:
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("""
+ query = """
SELECT
ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean
FROM
ProbeSetXRef, ProbeSet
WHERE
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
- ProbeSet.Name = "%s" AND
- ProbeSetXRef.ProbeSetFreezeId =%s
- """, (self.name, self.dataset.id)).fetchone()
+ ProbeSet.Name = "{}" AND
+ ProbeSetXRef.ProbeSetFreezeId ={}
+ """.format(self.name, self.dataset.id)
+ trait_qtl = g.db.execute(query).fetchone()
#self.cursor.execute(query)
- #traitQTL = self.cursor.fetchone()
- if traitQTL:
- self.locus, self.lrs, self.pvalue, self.mean = traitQTL
+ #trait_qtl = self.cursor.fetchone()
+ if trait_qtl:
+ self.locus, self.lrs, self.pvalue, self.mean = trait_qtl
+ if self.locus:
+ query = """
+ select Geno.Chr, Geno.Mb from Geno, Species
+ where Species.Name = '{}' and
+ Geno.Name = '{}' and
+ Geno.SpeciesId = Species.Id
+ """.format(self.dataset.group.species, self.locus)
+ print("query is:", query)
+ result = g.db.execute(query).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("""
+ trait_qtl = g.db.execute("""
SELECT
PublishXRef.Locus, PublishXRef.LRS
FROM
@@ -369,9 +408,9 @@ class GeneralTrait:
PublishFreeze.Id =%s
""", (self.name, self.dataset.id)).fetchone()
#self.cursor.execute(query)
- #traitQTL = self.cursor.fetchone()
- if traitQTL:
- self.locus, self.lrs = traitQTL
+ #trait_qtl = self.cursor.fetchone()
+ if trait_qtl:
+ self.locus, self.lrs = trait_qtl
else:
self.locus = self.lrs = ""
else:
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 03:01:40 +0000