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)