Created on Sep 28, 2014
@author: karmel
'''
from glasslab.dataanalysis.graphing.seq_grapher import SeqGrapher
from glasslab.dataanalysis.misc.rodrigo.samples import sample_name,\
get_threshold
if __name__ == '__main__':
yzer = SeqGrapher()
dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/' +\
'Miscellaneous_Collaborations/Rodrigo_CD8s_2014_09/Promoters'
dirpath = yzer.get_path(dirpath)
cond, seq, breed = ('naive', 'atac', '')
wt_prefix = sample_name(cond, seq, breed)
ko_prefix = sample_name(cond, seq, 'foxo1_ko_')
wt_dirpath = yzer.get_filename(dirpath, wt_prefix)
ko_dirpath = yzer.get_filename(dirpath, ko_prefix)
wt_filename = yzer.get_filename(wt_dirpath,
wt_prefix + '_promoters.txt')
ko_filename = yzer.get_filename(ko_dirpath,
ko_prefix + '_promoters.txt')
wt_data = yzer.import_file(wt_filename)
wt_data = wt_data.fillna(0)
ko_data = yzer.import_file(ko_filename)
ko_data = ko_data.fillna(0)
Created on Sep 27, 2014
@author: karmel
'''
from glasslab.dataanalysis.misc.rodrigo.samples import SAMPLES, sample_name,\
get_threshold
from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer
if __name__ == '__main__':
yzer = MotifAnalyzer()
dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/' +\
'Miscellaneous_Collaborations/Rodrigo_CD8s_2014_09/Enhancers'
dirpath = yzer.get_path(dirpath)
for cond, seq, breed in SAMPLES:
sample_prefix = sample_name(cond, seq, breed)
sample_dirpath = yzer.get_filename(dirpath, sample_prefix)
filename = yzer.get_filename(sample_dirpath,
sample_prefix + '_enhancers.txt')
data = yzer.import_file(filename)
data = data.fillna(0)
if True:
min_thresh = get_threshold(seq)
subdata = data[data['tag_count'] >= min_thresh]
yzer.run_homer(subdata,
'all',
sample_dirpath,