diff options
| -rw-r--r-- | wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 12 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/heatmap/heatmap.py | 37 | ||||
| -rw-r--r-- | wqflask/wqflask/network_graph/network_graph.py | 20 |
5 files changed, 9 insertions, 89 deletions
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py index 3e5daa50..16832621 100644 --- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py +++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py @@ -19,34 +19,16 @@ # 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 pickle -import os -import time -import pp -import math -import collections -import resource - - from pprint import pformat as pf from base.trait import create_trait 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 diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 233a3a03..5ced30b6 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -29,24 +29,16 @@ import rpy2.robjects as ro # R Objects from rpy2.robjects.packages import importr utils = importr("utils") -from pprint import pformat as pf - -from base import webqtlConfig -from utility.THCell import THCell -from utility.TDCell import TDCell -from base.trait import create_trait from base import data_set from utility import webqtlUtil, helper_functions, corr_result_helpers, hmac from db import webqtlDatabaseFunction -import utility.webqtlUtil #this is for parallel computing only. +import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions from utility.benchmark import Bench import utility.webqtlUtil -from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string - +from utility.type_checking import is_str, get_float, get_int, get_string from MySQLdb import escape_string as escape -from pprint import pformat as pf from flask import Flask, g diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index ea786289..bd5aca1f 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -20,19 +20,8 @@ from __future__ import absolute_import, print_function, division -import sys -# sys.path.append(".") Never do this in a webserver! - -import string -import pickle -import os import datetime -import time -import pp import math -import collections -import resource - import numpy as np import scipy diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 4fdc1f13..1f1cdb90 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -1,46 +1,19 @@ from __future__ import absolute_import, print_function, division -import sys -# sys.path.append(".") Never in a running webserver - import string -import pickle import os -import datetime -import time -import pp -import math import random -import collections -import resource - -import scipy -import numpy as np - -from pprint import pformat as pf - -from base.trait import GeneralTrait -from base import data_set from base import species from base import webqtlConfig from utility import helper_functions -from utility import Plot, Bunch -from utility import temp_data -from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR - -from MySQLdb import escape_string as escape - -import pickle as pickle -import simplejson as json - -from pprint import pformat as pf +from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR from redis import Redis -Redis = Redis() - from flask import Flask, g - from utility.logger import getLogger + +Redis = Redis() + logger = getLogger(__name__ ) class Heatmap(object): @@ -205,4 +178,4 @@ def parse_reaper_output(gwa_filename): marker['additive'] = float(line.split("\t")[6]) marker_obs.append(marker) - return marker_obs
\ No newline at end of file + return marker_obs diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py index 7916651f..2a4c4a93 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -20,27 +20,11 @@ from __future__ import absolute_import, print_function, division -import sys - -import string -import pickle -import os -import time -import pp -import math -import collections -import resource - import scipy - import simplejson as json - -from rpy2.robjects.packages import importr -import rpy2.robjects as robjects - from pprint import pformat as pf -from utility.THCell import THCell + from utility.TDCell import TDCell from base.trait import create_trait from base import data_set @@ -218,4 +202,4 @@ class NetworkGraph(object): trait_ob = create_trait(dataset=dataset_ob, name=trait_name, cellid=None) - self.trait_list.append((trait_ob, dataset_ob))
\ No newline at end of file + self.trait_list.append((trait_ob, dataset_ob)) |