'''
Created on Apr 12, 2013
@author: karmel
'''
from __future__ import division
from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer
if __name__ == '__main__':
yzer = MotifAnalyzer()
dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/CD4TCells/TReg_enhancers/2013_04_01'
dirpath = yzer.get_path(dirpath)
data = yzer.import_file(yzer.get_filename(
dirpath, 'th1_with_stat1_ko.txt')).fillna(0)
print len(data)
data = data[data['tss_id'] == 0]
data['ko_ratio'] = data['ko_id'] / data['th1_id']
data['treg_ratio'] = data['treg_id'] / data['th1_id']
enh = len(data)
print enh
print sum(data['ko_ratio'] < .5), sum(data['ko_ratio'] < .5) / enh
print sum(data['treg_ratio'] < .5), sum(data['treg_ratio'] < .5) / enh
print sum((data['treg_ratio'] < .5) & (data['ko_ratio'] < .5))
print sum((data['treg_ratio'] < .5) & (data['ko_ratio'] < .5)) / enh
'''
Created on Feb 8, 2013
@author: karmel
'''
from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer
if __name__ == '__main__':
yzer = MotifAnalyzer()
base_dirpath = yzer.get_path(
'karmel/GlassLab/Notes_and_Reports/NOD_BALBc/ThioMacs/Analysis_2013_02/'
)
dirpath = yzer.get_and_create_path(base_dirpath, 'motifs/')
filename = yzer.get_filename(base_dirpath, 'transcript_vectors.txt')
data = yzer.import_file(filename)
data = data.fillna(0)
# Promoters
if False:
refseq = data[data['has_refseq'] == 1]
refseq = refseq[refseq['transcript_score'] >= 4]
if True:
yzer.run_homer(refseq,
'refseq_promoter',
dirpath,
cpus=6,
center=False,
reverse=False,
preceding=True,
size=400,
