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## Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Dr. Robert W. Williams at rwilliams@uthsc.edu
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
from __future__ import absolute_import, print_function, division
import sys
# sys.path.append(".") Never do this in a webserver!
import string
import cPickle
import os
import time
import pp
import math
import collections
import resource
from pprint import pformat as pf
from htmlgen import HTMLgen2 as HT
import reaper
from base.trait import GeneralTrait
from base import data_set
from utility import webqtlUtil, helper_functions, corr_result_helpers
from db import webqtlDatabaseFunction
import utility.webqtlUtil #this is for parallel computing only.
from wqflask.correlation import correlation_functions
from utility.benchmark import Bench
from MySQLdb import escape_string as escape
from pprint import pformat as pf
from flask import Flask, g
class ComparisonBarChart(object):
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
self.all_sample_list = []
self.traits = []
self.insufficient_shared_samples = False
this_group = self.trait_list[0][1].group.name #ZS: Getting initial group name before verifying all traits are in the same group in the following loop
for trait_db in self.trait_list:
if trait_db[1].group.name != this_group:
self.insufficient_shared_samples = True
break
else:
this_group = trait_db[1].group.name
this_trait = trait_db[0]
self.traits.append(this_trait)
this_sample_data = this_trait.data
for sample in this_sample_data:
if sample not in self.all_sample_list:
self.all_sample_list.append(sample)
if self.insufficient_shared_samples:
pass
else:
self.sample_data = []
for trait_db in self.trait_list:
this_trait = trait_db[0]
this_sample_data = this_trait.data
this_trait_vals = []
for sample in self.all_sample_list:
if sample in this_sample_data:
this_trait_vals.append(this_sample_data[sample].value)
else:
this_trait_vals.append('')
self.sample_data.append(this_trait_vals)
self.js_data = dict(traits = [trait.name for trait in self.traits],
samples = self.all_sample_list,
sample_data = self.sample_data,)
def get_trait_db_obs(self, trait_db_list):
self.trait_list = []
for i, trait_db in enumerate(trait_db_list):
if i == (len(trait_db_list) - 1):
break
trait_name, dataset_name = trait_db.split(":")
#print("dataset_name:", dataset_name)
dataset_ob = data_set.create_dataset(dataset_name)
trait_ob = GeneralTrait(dataset=dataset_ob,
name=trait_name,
cellid=None)
self.trait_list.append((trait_ob, dataset_ob))
#print("trait_list:", self.trait_list)
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