diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rwxr-xr-x | wqflask/base/data_set.py | 29 |
1 files changed, 27 insertions, 2 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 8ced1528..182e15e6 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -23,6 +23,8 @@ from __future__ import absolute_import, print_function, division import os +import json + from flask import Flask, g from htmlgen import HTMLgen2 as HT @@ -64,6 +66,21 @@ def create_dataset(dataset_name): return dataset_class(dataset_name) +class Markers(object): + """Todo: Build in cacheing so it saves us reading the same file more than once""" + def __init__(self, name): + json_data_fh = open(os.path.join(webqtlConfig.NEWGENODIR + name + '.json')) + self.markers = json.load(json_data) + + def add_pvalues(p_values): + #for count, marker in enumerate(self.markers): + # marker['p_value'] = p_values[count] + + for marker, p_value in itertools.izip(self.markers, p_values): + marker['p_value'] = p_value + #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values + marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 + class DatasetGroup(object): """ Each group has multiple datasets; each species has multiple groups. @@ -84,6 +101,7 @@ class DatasetGroup(object): self.f1list = None self.parlist = None self.allsamples = None + self.markers = Markers(self.name) #def read_genotype(self): @@ -91,9 +109,16 @@ class DatasetGroup(object): # # if not self.genotype: # Didn'd succeed, so we try method 2 # self.read_genotype_data() - + + #def read_genotype_json(self): + # '''Read genotype from json file''' + # + # json_data = open(os.path.join(webqtlConfig.NEWGENODIR + self.name + '.json')) + # markers = json.load(json_data) + # + def read_genotype_file(self): - '''read genotype from .geno file instead of database''' + '''Read genotype from .geno file instead of database''' #if self.group == 'BXD300': # self.group = 'BXD' # |