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,