%pylab inline

"""
Explanation: Global Imports
End of explanation
"""


import os as os
import pickle as pickle
import pandas as pd

print 'changing to source dirctory'

os.chdir('../src')

import Data.Firehose as FH

"""
Explanation: External Package Imports
End of explanation
"""


from IPython import utils  
from IPython.display import HTML 

css_file = 'profile_default/static/custom/custom.css'
base = utils.path.get_ipython_dir()
styles = "<style>\n%s\n</style>" % (open(os.path.join(base, css_file),'r').read())
display(HTML(styles))

"""
Explanation: Tweaking Display Parameters
Load default custom.css file from ipython profile
End of explanation
"""


pd.set_option('precision', 3)
pd.set_option('display.width', 300)
plt.rcParams['font.size'] = 12

"""
Explanation: Pandas display parameters
End of explanation
"""


'''Color schemes for paper taken from http://colorbrewer2.org/'''
colors = plt.rcParams['axes.color_cycle']
colors_st = ['#CA0020', '#F4A582', '#92C5DE', '#0571B0']
colors_th = ['#E66101', '#FDB863', '#B2ABD2', '#5E3C99']

"""
Explanation: Tweaking color scheme
End of explanation
"""


OUT_PATH = '../Data'
RUN_DATE = '2014_07_15'
VERSION = 'all'
CANCER = 'HNSC'
FIGDIR = '../Figures/'
if not os.path.isdir(FIGDIR):
    os.makedirs(FIGDIR)

DESCRIPTION = '''Updating analysis for updated dataset.'''

PARAMETERS = {'min_patients' : 12,
              'pathway_file' : '../ExtraData/c2.cp.v3.0.symbols_edit.csv'
              }

#GENE_POS = pd.read_csv('../ExtraData/HGNC_chr_pos.txt')
#GENE_LIST_FILE = '../ExtraData/HGNC_Genes'
#GENES = open(GENE_LIST_FILE, 'rb').read().split('\n')

"""
Explanation: Global Run Variables
<span class='altert alert-success' style='font-size:120%'>Change OUT_PATH to directory on your machine where you want to store the data</span>
End of explanation
"""


