autoxlim = False # True or False if __name__ == '__main__': if len(sys.argv) < 3: print('Tandem dupes file and TSS data must be given on the command line.') sys.exit() starttime = time.time() tandem_fname = sys.argv[1] genome_fname = sys.argv[2] tandem_path = os.path.join(_input_dir, tandem_fname) 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 = []
# Set constants chromosome_list = [str('chr%s' %i) for i in range(1, 23)] chromosome_list.append('chrX') chromosome_list.append('chrY') # plot_output_fname = 'tandem_dupe_chr_distribution.pdf' if __name__ == '__main__': if len(sys.argv) < 3: print('Tandem dupes file and TSS data must be given on the command line.') sys.exit() starttime = time.time() tandem_fname = sys.argv[1] genome_fname = sys.argv[2] tandem_path = os.path.join(_input_dir, tandem_fname) genome_path = os.path.join(_input_dir, genome_fname) all_tss = genome_info.get_all_tss_locations(genome_path, 'chrom', 'txStart', chromosome_list) all_tandem_dupes_pairs = tandem_data.tandem_dupes_all_pairs(tandem_path, 'start_1', 'end_1', 'chromosome_1', chromosome_list) for chromosome in chromosome_list: full_save_path = os.path.join(_plot_dir, 'tandem_dupe_chr_distribution_%s.pdf' %chromosome) jplots.plot_tandem_tss(all_tandem_dupes_pairs, all_tss, chromosome, full_save_path)