''' Created on Jun 27, 2014 @author: karmel ''' from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/AND_TCR/Analysis/Chips1_2_3/Motifs' dirpath = yzer.get_path(dirpath) for ab in ('me2', 'ac'): datasets = [] for peptide in ('K99A', 'NoPep', 'PCC'): pep_dirpath = yzer.get_filename(dirpath, '{}_{}'.format(peptide, ab)) filename = yzer.get_filename( pep_dirpath, '{}_{}_enhancers.txt'.format(peptide, ab)) data = yzer.import_file(filename) data = data.fillna(0) # Only in all three reps #data = data[(data['p1_id'] > 0) & (data['p2_id'] > 0) & (data['p3_id'] > 0)] datasets.append(data) # ONLY this pep: only = sum((data['id(2)'] == 0) & (data['id(3)'] == 0))
''' Created on Mar 28, 2013 @author: karmel ''' 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_03_19' dirpath = yzer.get_path(dirpath) motif_dirpath = yzer.get_filename(dirpath, 'motifs') for antibody in ('me2', 'ac'): treg = yzer.import_file( yzer.get_filename( dirpath, 'treg_with_naive_{0}.txt'.format(antibody))).fillna(0) naive = yzer.import_file( yzer.get_filename( dirpath, 'naive_with_treg_{0}.txt'.format(antibody))).fillna(0) # Filter out promoters treg = treg[treg['tss_id'] == 0] naive = naive[naive['tss_id'] == 0] # Get venn-diagram sets for foxp3/me2 only_treg = treg[treg['naive_id'] == 0] only_naive = naive[naive['treg_id'] == 0] shared = treg[treg['naive_id'] > 0] print len(only_treg), len(only_naive), len(shared)
''' Created on Sep 7, 2012 @author: karmel ''' from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/Classes/Rotations/Finland_2012/GR_Project/' dirpath = yzer.get_path(dirpath) motif_dirpath = yzer.get_filename(dirpath, 'motifs', 'from_peaks') all_data = yzer.import_file( yzer.get_filename(motif_dirpath, 'p65_kla_vectors.txt')) size = 100 if True: for ratio in (3, 2, 1.5): enhancers = yzer.import_file( yzer.get_filename( dirpath, 'boxplots_non_refseq_by_p65', 'enhancer_like_lose_p65_{0}x_change_dsg_only.txt'.format( ratio))) enhancers['glass_transcript_id'] = enhancers['id'] # Limit to peaks and touching transcripts, then pull out peaks that intersect our enhancer set data = all_data[all_data['touches'] == 't'] data = data.merge(enhancers, how='right', on='glass_transcript_id',
grapher.get_filename( scatter_dirpath, 'two_color_kla_vs_kla_dex_group_{0}_runs_{1}.png'. format(x, slug_label))) grapher.show_plot() if False: # Gene names print grapher.get_gene_names(refseq[(refseq['kla_1_lfc'] >= 1)], add_quotes=True) print grapher.get_gene_names( refseq[(refseq['kla_1_lfc'] >= 1) & (refseq['dex_over_kla_1_lfc'] < -.58)]) if False: yzer = MotifAnalyzer() motif_dirpath = yzer.get_filename(dirpath, 'motifs/size_200') distal = data[data['distal'] == 't'] dataset = distal[(distal['kla_lfc'] >= 1)] yzer.prep_files_for_homer(dataset, 'distal_up_in_kla_all', motif_dirpath, center=False, reverse=False, preceding=True, size=200) dataset = distal[(distal['kla_1_lfc'] >= 1)] yzer.prep_files_for_homer(dataset, 'distal_up_in_kla_1',
''' Created on Nov 7, 2012 @author: karmel ''' from __future__ import division from glasslab.dataanalysis.misc.cd4tcell_finland_2012.resources import replicate_sets from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/CD4TCells_Finland_2012/Analysis_2013_02' dirpath = yzer.get_path(dirpath) go_path = yzer.get_and_create_path(dirpath, 'with_me3', 'go_analysis', '0_8_min_lfc') data = yzer.import_file( yzer.get_filename(dirpath, 'transcript_vectors.txt')) data = data.fillna(0) data = data[data['naive_me3_tag_count'] + data['act_me3_tag_count'] > 0] if False: curr_path = yzer.get_and_create_path(dirpath, 'with_me3', 'motif_analysis') yzer.run_homer(data, 'all_refseq_preceding', curr_path, center=False, reverse=False, preceding=True,
''' Created on Oct 5, 2014 @author: karmel ''' from glasslab.dataanalysis.misc.rodrigo.samples import get_threshold,\ get_breed_sets 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_set2' dirpath = yzer.get_path(dirpath) datasets = {} breed_sets = get_breed_sets() # Working with only WT for now sample_names, short_names = breed_sets[0] # Set up our samples datasets = {} for sample_prefix in short_names: 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)
''' 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',
''' Created on Feb 12, 2013 @author: karmel ''' from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/AND_TCR/Analysis/IDR/Motifs' dirpath = yzer.get_path(dirpath) for ab in ('me2', ): #'ac'): for peptide in ('K99A', 'NoPep', 'PCC'): pep_dirpath = yzer.get_filename(dirpath, '{}_{}'.format(peptide, ab)) if True: filename = yzer.get_filename( pep_dirpath, '{}_{}_enhancers.txt'.format(peptide, ab)) data = yzer.import_file(filename) data = data.fillna(0) if True: yzer.run_homer(data, 'all', pep_dirpath, cpus=8, center=True,
''' Created on Feb 12, 2013 @author: karmel ''' from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/CD4TCells/H3K4me2/Analysis' dirpath = yzer.get_path(dirpath) motif_dirpath = yzer.get_filename(dirpath, 'motifs') filename = yzer.get_filename(dirpath, 'thio_peak_vectors.txt') data = yzer.import_file(filename) data = data.fillna(0) # me2 if True: if False: yzer.run_homer(data, 'thio_all', motif_dirpath, cpus=6, center=True, reverse=False, preceding=False, size=200, length=[8, 10, 12, 15]) data = data[data['tss_id'] == 0]
''' Created on Feb 12, 2013 @author: karmel Note that set 1 of Rudensky's Foxp3 chip has 2x as many peaks, but he seems to use set 2 in the paper (?). Here we use summed tags and peaks found in that. ''' from __future__ import division from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer from glasslab.dataanalysis.graphing.seq_grapher import SeqGrapher if __name__ == '__main__': yzer = MotifAnalyzer() grapher = SeqGrapher() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/CD4TCells/TReg_enhancers/2013_04_01' dirpath = yzer.get_path(dirpath) motif_dirpath = yzer.get_filename(dirpath, 'motifs') graph_dirpath = yzer.get_filename(dirpath, 'piecharts') min_score = 10 for antibody in ('me2', ): data = {} celltypes = ['treg', 'naive', 'th1', 'th2'] for celltype in ('treg', 'th1'): data[celltype] = yzer.import_file( yzer.get_filename( dirpath, '{0}_{1}_versus_others_with_foxp3.txt'.format( celltype, antibody))).fillna(0)
''' Created on Feb 12, 2013 @author: karmel ''' from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/CD4TCells/iTreg_enhancers/2014_04_11/' dirpath = yzer.get_path(dirpath) for ab in ('me2', 'ac'): condition = 'treg' motif_dirpath = yzer.get_filename(dirpath, 'Motifs') filename = yzer.get_filename( dirpath, '{}_{}_enhancers.txt'.format(condition, ab)) data = yzer.import_file(filename) data = data.fillna(0) min_thresh = 20 if False: subdata = data[data['tag_count'] > min_thresh] subdata = subdata[subdata['tag_count(2)'] > min_thresh] subdata = subdata[subdata['tag_count(3)'] <= 0] subdata = subdata[subdata['tag_count(4)'] <= 0] subdir = 'treg_shared_' + ab
''' Created on Feb 12, 2013 @author: karmel ''' 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_03_19' dirpath = yzer.get_path(dirpath) motif_dirpath = yzer.get_filename(dirpath, 'motifs') for antibody in ('me2', ): data = {} celltypes = ['treg', 'naive', 'th1', 'th2'] for celltype in celltypes: data[celltype] = yzer.import_file( yzer.get_filename( dirpath, '{0}_{1}_versus_others.txt'.format(celltype, antibody))).fillna(0) # Filter out promoters data[celltype] = data[celltype][data[celltype]['tss_id'] == 0] # Get venn-diagram "only" sets others = celltypes[:] others.remove(celltype)
''' Created on Sep 27, 2014 @author: karmel ''' from glasslab.dataanalysis.misc.rodrigo.samples import 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/Promoters' dirpath = yzer.get_path(dirpath) cond, seq, breed = ('naive', 'atac', '') sample_prefix = sample_name(cond, seq, breed) sample_dirpath = yzer.get_filename(dirpath, sample_prefix) filename = yzer.get_filename(sample_dirpath, sample_prefix + '_promoters.txt') data = yzer.import_file(filename) data = data.fillna(0) min_thresh = get_threshold(seq) data = data[data['tag_count'] >= min_thresh] fold = 2 if True: # ATAC peaks that are absent in the FOXO1 KO foxo1_critical = data[
''' Created on Sep 27, 2014 @author: karmel ''' from glasslab.dataanalysis.misc.rodrigo.samples import 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) cond, seq, breed = ('naive', 'foxo1', '') 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) min_thresh = get_threshold(seq) data = data[data['tag_count'] >= min_thresh] fold = 2 if True: naive_only = data[data['lcmv_d12_foxo1_tag_count'] < min_thresh] yzer.run_homer(naive_only,
l + '\n(count: {0})'.format(len(v)) for l, v in zip(labels, vals) ] title = 'Balbc vs NOD Log-fold Change According to SRF Binding' if True: ax = yzer.boxplot( vals, labels, title=title, xlabel='Transcript subset', ylabel='log2(NOD notx 1h GRO-seq/BALBc notx 1h GRO-seq)', show_outliers=False, show_plot=True, wide=True, save_dir=img_dirpath) if False: yzer = MotifAnalyzer() motifs_dirpath = yzer.get_filename(dirpath, 'motifs') # Motif finding for enhancers with SRF bg = yzer.get_filename( motifs_dirpath, 'enhancer_at_least_10_tags_15/enhancer_at_least_10_tags_15_regions_for_homer.txt' ) enh_with_srf = datasets[4] yzer.run_homer(enh_with_srf, 'enhancer_with_srf', motifs_dirpath, cpus=6, center=False, reverse=False, preceding=False,
''' Created on Feb 20, 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/Rudensky_enhancers' dirpath = yzer.get_path(dirpath) motifs_dirpath = yzer.get_and_create_path(dirpath, 'motifs') peak_pretty = 'Foxp3' peak = peak_pretty.lower() foxp3 = yzer.import_file( yzer.get_filename(dirpath, '{0}_1_with_naive_me2.txt'.format(peak))).fillna(0) naive = yzer.import_file( yzer.get_filename(dirpath, 'naive_me2_with_{0}.txt'.format(peak))).fillna(0) # Filter out promoters foxp3 = foxp3[foxp3['tss_id'] == 0] naive = naive[naive['tss_id'] == 0] # Get venn-diagram sets for foxp3/me2 only_foxp3 = foxp3[foxp3['naive_id'] == 0] only_naive = naive[naive['foxp3_1_id'] == 0]
''' Created on Jul 4, 2012 @author: karmel The goal here is to see if we can tease out which features are predictive of characteristics of interest, such as pausing ratio or transrepression. Worth a stab. ''' from glasslab.dataanalysis.misc.gr_project_2012.elongation import get_rep_string import sys from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/Classes/Rotations/Finland_2012/GR_Project/motifs' dirpath = yzer.get_path(dirpath) grouped = yzer.import_file( yzer.get_filename(dirpath, 'feature_vectors.txt')) paused = [] if True: # Can we predict pausing ratio? # Minimal ratio in KLA+Dex vs. KLA pausing try: min_ratio = float(sys.argv[1]) except IndexError: min_ratio = 2 try:
''' Created on Sep 7, 2012 @author: karmel ''' from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/Classes/Rotations/Finland_2012/GR_Project/motifs' dirpath = yzer.get_path(dirpath) motif_dirpath = yzer.get_filename(dirpath,'from_peaks') transcripts = yzer.import_file(yzer.get_filename(dirpath, 'transcript_vectors.txt')) transcripts['glass_transcript_id'] = transcripts['id'] for peak_type in ('gr_dex', 'gr_kla_dex', 'p65_kla_dex','p65_kla'): size = 100 if True: all_data = yzer.import_file(yzer.get_filename(motif_dirpath, '{0}_vectors.txt'.format(peak_type))) all_data = all_data.merge(transcripts, how='left', on='glass_transcript_id',suffixes=['','trans']) all_data = all_data.fillna(0) for super_name, data in (#('all', all_data,), #('refseq', all_data[(all_data['score'] > 10) & (all_data['has_refseq'] == 1) # & (all_data['touches'] == 't') | (all_data['relationship'] == 'is downstream of')],), #('distal', all_data[(all_data['distal'] == 't')],),
''' Created on Mar 1, 2014 @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/iTreg_enhancers/2014_02_14/Motifs' dirpath = yzer.get_path(dirpath) for ab in ('me2', 'ac'): for condition in ('treg', 'itreg'): cond_dirpath = yzer.get_filename(dirpath, '{}_{}'.format(condition, ab)) filename = yzer.get_filename( cond_dirpath, '{}_{}_enhancers.txt'.format(condition, ab)) data = yzer.import_file(filename) data = data.fillna(0) print('Total {} {}'.format(condition, ab)) print(len(data)) min_thresh = 20 if True: data = data[data['tag_count'] > min_thresh]
''' 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,
@author: karmel Output TSV for all of the WT and Foxo1 KO ATAC seq samples from the LCMV timecourse. If running on Mac, make sure psycopg2 is set up: sudo ln -s /Library/PostgreSQL/9.2/lib/libssl.1.0.0.dylib /usr/lib sudo ln -s /Library/PostgreSQL/9.2/lib/libcrypto.1.0.0.dylib /usr/lib ''' from glasslab.dataanalysis.misc.rodrigo.samples import get_breed_sets from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer from glasslab.utils.database import get_engine, dataframe_from_query if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/' +\ 'Miscellaneous_Collaborations/Rodrigo_CD8s_2014_09/Enhancers_set2' dirpath = yzer.get_path(dirpath) # Get DB engine engine = get_engine(uri='ec2-23-20-125-153.compute-1.amazonaws.com', password='******') breed_sets = get_breed_sets() # Run and save output from sql queries for k, (samples, short_names) in enumerate(breed_sets): oth_breed = breed_sets[1 - k] for i, sample in enumerate(samples):
''' Created on Feb 12, 2013 @author: karmel ''' from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/AND_TCR/Analysis/Chips1_2/Motifs' dirpath = yzer.get_path(dirpath) for ab in ('me2', 'ac'): for peptide in ('K99A', 'NoPep', 'PCC'): pep_dirpath = yzer.get_filename(dirpath, '{}_{}'.format(peptide, ab)) if False: filename = yzer.get_filename( pep_dirpath, '{}_{}_enhancers.txt'.format(peptide, ab)) data = yzer.import_file(filename) data = data.fillna(0) yzer.run_homer(data, 'all', pep_dirpath, cpus=6, center=True, reverse=False,
''' Created on Jul 5, 2012 @author: karmel ''' from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer from glasslab.dataanalysis.misc.gr_project_2012.elongation import get_rep_string import sys if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/Classes/Rotations/Finland_2012/GR_Project/motifs' dirpath = yzer.get_path(dirpath) pausing_data = yzer.import_file( yzer.get_filename(dirpath, 'feature_vectors.txt')) data = yzer.import_file( yzer.get_filename(dirpath, 'transcript_vectors.txt')) try: min_ratio = float(sys.argv[1]) except IndexError: min_ratio = 1.5 if False: yzer.prep_files_for_homer(data, 'all_transcripts_promoter', dirpath, center=False, reverse=False, preceding=True,
''' Created on Jul 4, 2012 @author: karmel ''' from __future__ import division from glasslab.dataanalysis.misc.gr_project_2012.elongation import get_rep_string import sys from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer from glasslab.dataanalysis.graphing.seq_grapher import SeqGrapher if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/Classes/Rotations/Finland 2012/KLA skew/' dirpath = yzer.get_path(dirpath) grouped = yzer.import_file( yzer.get_filename(dirpath, 'feature_vectors.txt')) repressed = [] if True: # Can we predict pausing ratio? # Minimal ratio in KLA+Dex vs. KLA pausing try: min_ratio = float(sys.argv[1]) except IndexError: min_ratio = -1 try: thresh = int(sys.argv[3])
''' Created on Feb 12, 2013 @author: karmel ''' from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/CD4TCells/iTreg_enhancers/2014_02_14/Motifs' dirpath = yzer.get_path(dirpath) for ab in ('me2', 'ac'): for condition in ('treg', 'itreg', 'activated'): cond_dirpath = yzer.get_filename(dirpath, '{}_{}'.format(condition, ab)) if True: filename = yzer.get_filename( cond_dirpath, '{}_{}_enhancers.txt'.format(condition, ab)) data = yzer.import_file(filename) data = data.fillna(0) yzer.run_homer(data, 'all', cond_dirpath, cpus=6, center=True, reverse=False,
''' Created on Feb 12, 2013 @author: karmel ''' from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/CD4TCells/iTreg_enhancers/2014_02_14/Motifs' dirpath = yzer.get_path(dirpath) for ab in ('me2', 'ac'): for condition in ('treg', 'itreg', 'activated'): cond_dirpath = yzer.get_filename(dirpath, '{}_{}'.format(condition, ab)) if False: filename = yzer.get_filename( cond_dirpath, '{}_{}_enhancers.txt'.format(condition, ab)) data = yzer.import_file(filename) data = data.fillna(0) min_thresh = 20 data = data[data['tag_count'] > min_thresh] yzer.run_homer(data, 'filtered_{}'.format(min_thresh), cond_dirpath, cpus=6,
''' Created on Jul 4, 2012 @author: karmel ''' from glasslab.dataanalysis.misc.gr_project_2012.elongation import get_rep_string import sys from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer from glasslab.dataanalysis.graphing.seq_grapher import SeqGrapher if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/Classes/Rotations/Finland 2012/KLA skew/' dirpath = yzer.get_path(dirpath) grouped = yzer.import_file( yzer.get_filename(dirpath, 'feature_vectors.txt')) repressed = [] if True: # Can we predict pausing ratio? # Minimal ratio in KLA+Dex vs. KLA pausing try: min_ratio = float(sys.argv[1]) except IndexError: min_ratio = -1 try: thresh = int(sys.argv[3]) except IndexError:
''' Created on Feb 12, 2013 @author: karmel Note that set 1 of Rudensky's Foxp3 chip has 2x as many peaks, but he seems to use set 2 in the paper (?). Here we use summed tags and peaks found in that. ''' from __future__ import division from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer from collections import OrderedDict if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/CD4TCells/TReg_enhancers/2013_04_01' dirpath = yzer.get_path(dirpath) motif_dirpath = yzer.get_filename(dirpath, 'motifs') min_score = 10 stats = OrderedDict() all_data = yzer.import_file( yzer.get_filename(dirpath, 'foxp3_with_treg_enhancers.txt')).fillna(0) stats['all'] = len(all_data) # Filter out promoters data = all_data[all_data['tss_id'] == 0] stats['enhancers'] = len(data) stats['me2_treg'] = sum(data['me2_id'] > 0) stats['ac_treg'] = sum(data['ac_id'] > 0)
''' 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 Oct 2, 2014 @author: karmel Output TSV for all of the WT and Foxo1 KO ATAC seq samples from the first dataset. ''' from glasslab.dataanalysis.misc.rodrigo.samples import SAMPLES, sample_name from glasslab.dataanalysis.motifs.motif_analyzer import MotifAnalyzer from glasslab.utils.database import get_engine, dataframe_from_query if __name__ == '__main__': yzer = MotifAnalyzer() dirpath = 'karmel/Desktop/Projects/GlassLab/Notes_and_Reports/' +\ 'Miscellaneous_Collaborations/Rodrigo_CD8s_2014_09/Promoters' dirpath = yzer.get_path(dirpath) # Get DB engine engine = get_engine(uri='ec2-23-20-125-153.compute-1.amazonaws.com', password='******') for i, (cond, seq, breed) in enumerate(SAMPLES): others = SAMPLES[:i] + SAMPLES[i + 1:] sql = '''select distinct on (p1.id) chr."name" as chr_name, p1."start", p1."end", p1.tag_count, p1.*, ''' selects, joins = [], [] for j, (oth_cond, oth_seq, oth_breed) in enumerate(others): counter = j + 2