diff options
Diffstat (limited to 'wqflask/base/trait.py')
| -rwxr-xr-x | wqflask/base/trait.py | 35 |
1 files changed, 26 insertions, 9 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index dde8b8d8..7847c0a6 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 @@ -15,7 +17,11 @@ 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 @@ -23,8 +29,12 @@ class GeneralTrait: """ 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. 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') @@ -39,8 +49,6 @@ 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 @@ -78,7 +86,7 @@ class GeneralTrait: #desc = self.handle_pca(desc) stringy = desc return stringy - + def display_name(self): @@ -269,7 +277,7 @@ 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 +295,7 @@ 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,','), @@ -355,8 +363,17 @@ 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 |