''' Created on Sep 7, 2012 @author: karmel ''' from __future__ import division from glasslab.dataanalysis.graphing.seq_grapher import SeqGrapher if __name__ == '__main__': grapher = SeqGrapher() base_dirpath = 'karmel/Desktop/Projects/Classes/Rotations/Finland_2012/GR_Project/' base_dirpath = grapher.get_path(base_dirpath) dirpath = grapher.get_filename(base_dirpath, 'motifs') filename = grapher.get_filename(dirpath, 'transcript_vectors.txt') data = grapher.import_file(filename) # Boxplots for gr_dex peaks by lfc in Dex if False: #data = data[data['distal'] == 't'] data = data[data['has_refseq'] == 1] down = data[data['dex_1_lfc'] <= -1] up = data[data['dex_1_lfc'] >= 1] nc = data[abs(data['dex_1_lfc']) < 1] key = 'p65_kla_tag_count' datasets = [down[key],nc[key],up[key]] datasets = [d['p65_kla_dex_tag_count'] - d[key] for d in [down, nc, up]]
''' Created on Jan 30, 2013 @author: karmel ''' from __future__ import division from glasslab.dataanalysis.graphing.seq_grapher import SeqGrapher from collections import OrderedDict if __name__ == '__main__': yzer = SeqGrapher() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/HiC/' dirpath = yzer.get_path(dirpath) data_dirpath = yzer.get_filename(dirpath, 'enhancer_rewiring_lfc') transcripts = yzer.import_file( yzer.get_filename(dirpath, 'enhancer_sets', 'transcript_vectors.txt')) sets = OrderedDict(( ('all', yzer.import_file(yzer.get_filename(data_dirpath, 'all_vectors.cdt'))), #('all_6h', yzer.import_file(yzer.get_filename(data_dirpath,'kla_6h','all_vectors.cdt'))), ('rewired', yzer.import_file( yzer.get_filename(data_dirpath, 'rewired_vectors.cdt'))), #('rewired_6h', yzer.import_file(yzer.get_filename(data_dirpath,'kla_6h','rewired_vectors.cdt'))), ('shared', yzer.import_file(yzer.get_filename(data_dirpath, 'shared_vectors.cdt'))), )) for key, val in sets.items():
''' Created on Mar 4, 2013 @author: karmel ''' from __future__ import division from glasslab.dataanalysis.graphing.seq_grapher import SeqGrapher if __name__ == '__main__': yzer = SeqGrapher() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/NOD_BALBc/ThioMacs/Analysis_2013_02/' dirpath_bmdc = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/NOD_BALBc/BMDCs/Analysis_2013_03/' dirpath = yzer.get_path(dirpath) dirpath_bmdc = yzer.get_path(dirpath_bmdc) img_dirpath = yzer.get_and_create_path(dirpath, 'bmdc_vs_thiomac') thio = yzer.import_file( yzer.get_filename(dirpath, 'transcript_vectors.txt')) bmdc = yzer.import_file( yzer.get_filename(dirpath_bmdc, 'transcript_vectors.txt')) sets = [] for data in (thio, bmdc): data = data.fillna(0) refseq = yzer.get_refseq(data) # Remove low tag counts #refseq = refseq[refseq['transcript_score'] >= 4]
''' Created on Jun 26, 2012 @author: karmel ''' from glasslab.dataanalysis.misc.gr_project_2012.elongation import set_up_sequencing_run_ids, \ get_sequencing_run_id_sets, get_rep_string, total_tags_per_run from glasslab.dataanalysis.graphing.seq_grapher import SeqGrapher from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer if __name__ == '__main__': grapher = SeqGrapher() dirpath = 'karmel/Desktop/Projects/Classes/Rotations/Finland_2012/GR_Project/' dirpath = grapher.get_path(dirpath) filename = grapher.get_filename(dirpath, 'transcript_vectors.txt') data = grapher.import_file(filename) run_ids = set_up_sequencing_run_ids() dmso, kla, kla_dex, all_dmso, all_kla, all_kla_dex = get_sequencing_run_id_sets( ) total_tags = total_tags_per_run() # Norm sum scalars listed for all, group 1, group 2, group 3, group 4 kla_scalars = [1.223906, 1.281572, 1.118363, 1.104860, 1.503260] kla_dex_scalars = [1.182574, 1.147695, 1.248636, 1.069588, 1.388871] dex_over_kla_scalars = [1.069073, 0.967659, 1.122628, 1.008758, 0.927466] for i, scalar in enumerate(kla_scalars): data = grapher.normalize(data, 'kla_{0}tag_count'.format(get_rep_string(i)),
''' Created on Jul 2, 2014 @author: karmel We want to compare acetylation at various subsets of me2 enhancers. ''' from __future__ import division from glasslab.dataanalysis.graphing.seq_grapher import SeqGrapher if __name__ == '__main__': yzer = SeqGrapher() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/AND_TCR/Analysis/Chips1_2_3/Motifs' dirpath = yzer.get_path(dirpath) savepath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/AND_TCR/Analysis/Chips1_2_3/Figures/Acetyl_box_plots' savepath = yzer.get_path(savepath) if False: peptide, ab = 'PCC', 'me2' pep_dirpath = yzer.get_filename(dirpath, '{}_{}'.format(peptide, ab)) filename = yzer.get_filename( pep_dirpath, '{}_{}_enhancers_with_ac.txt'.format(peptide, ab)) data = yzer.import_file(filename) data = data.fillna(0) de_novo = data[data['no_pep_tag_count'] == 0] established = data[data['no_pep_tag_count'] > 0]
''' Created on Apr 3, 2012 @author: karmel ''' from __future__ import division import os from glasslab.dataanalysis.graphing.seq_grapher import SeqGrapher if __name__ == '__main__': yzer = SeqGrapher() dirpath = yzer.get_path('/karmel/Desktop/Projects/Classes/Rotations/Winter 2012/Endpoint analysis/for_minna/') filename = os.path.join(dirpath, 'merged_h3k4me2_notx.txt') data = yzer.import_file(filename) data['rpkm'] = 1000*data['trans']/data['width'] data = data.fillna(0) data = data[data['refseq'] == 0] me2_tf = data[(data['pu_1'] + data['cebpa'] + data['p65'] > 0) & (data['ctcf'] == 0) & (data['k27'] == 0) & (data['me2'] > 0) ] ctcf_tf = data[(data['pu_1'] + data['cebpa'] + data['p65'] > 0) & (data['ctcf'] > 0) & (data['k27'] == 0) & (data['me2'] == 0) ]
''' Created on Mar 23, 2012 @author: karmel ''' from __future__ import division from glasslab.dataanalysis.graphing.seq_grapher import SeqGrapher import os from scipy.stats.stats import ttest_ind if __name__ == '__main__': grapher = SeqGrapher() dirpath = grapher.get_path( '/karmel/Desktop/Projects/GlassLab/Notes_and_Reports/Inbred strains/Groseq comparisons/' ) filename = os.path.join(dirpath, 'groseq_with_h3k4me2.txt') data = grapher.import_file(filename) data = data.fillna(0) nod_norm, balb_norm = 0.393529, 0.359488 nod_to_balb_norm = 1.102844 data = grapher.normalize(data, 'balb_tag_count', nod_norm) data = grapher.normalize(data, 'nod_tag_count', balb_norm) print len(data) data['nod_with_bl6'] = data['nod_sv_id'] <= .1