''' 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,