genome_path = os.path.join(_input_dir, genome_fname) all_tss = genome_info.get_all_tss_locations(genome_path, genomedat_chrcolname, genomedat_startcolname, chromosome_list) all_tandem_dupes = tandem_data.tandem_dupes_all(tandem_path, tandem_position_colname, tandem_chrcolname, all_tss, chromosome_list) min_dists, closest_tss = integrate_data.calc_tss_dist(all_tandem_dupes, all_tss, chromosome_list, text_output_path) min_dists_list = [] for min_dists_chr_list in min_dists.values(): min_dists_list.extend(min_dists_chr_list) lessthan2kb, btwn2kb10kb, grtrthan10kb = \ integrate_data.bin_distances(min_dists_list) # print len(lessthan2kb), len(btwn2kb10kb), len(grtrthan10kb) jplots.plot_binned_bar_graph(min_dists_list, bins_in_plot, xmin, xmax, 'Min Distance to %s' %genomedat_startcolname,
print('TSS data must be given on the command line.') sys.exit() genome_fname = sys.argv[1] genome_path = os.path.join(_input_dir, genome_fname) chromosome_list = chr_tools.get_chr_list() all_tss = genome_info.get_all_tss_locations(genome_path, genome_chrcolname, genome_startcolname, chromosome_list) random_locs = random_genome_locs.generate_random_chr_pos(numb_rands_per_chr) tss_distances_dict, _ = integrate_data.calc_tss_dist(random_locs, all_tss, chromosome_list, os.path.join(_output_dir, output_filename)) '' tss_distances_list = [] for dist_list in tss_distances_dict.values(): # Each value is a list tss_distances_list.extend(dist_list) lessthan2kb, btwn2kb10kb, grtrthan10kb = \ integrate_data.bin_distances(tss_distances_list) # print lessthan2kb, btwn2kb10kb, grtrthan10kb ''' with open(os.path.join(_output_dir, output_filename), 'wb') as writefile: outwriter = csv.writer(writefile, delimiter='\t') for dist in tss_distances_list: