def loh(): """Make data for Murim's plots and call function to plot them""" plots = {} os.system('mkdir -p working/loh/') os.system('mkdir -p working/loh/all_non_ref_hg19') os.system('mkdir -p plots/loh/') os.system('mkdir -p plots/loh/all_non_ref_hg19/') quality_cutoff = float(100) coverage_cutoff = 8 samples2data = call_class.get_data_for_paired_samples() for sample in samples2data: freq_diffs = call_class.get_allele_freq_diffs_for_loh(samples2data[sample], quality_cutoff, coverage_cutoff) all_exome_freq_diffs = {} for exome in freq_diffs: plot_file = 'plots/loh/all_non_ref_hg19/' + exome + '.' + sample + '.png' input_file = 'working/loh/all_non_ref_hg19/' + exome + '.' + sample plot_loh(freq_diffs[exome], plot_file, input_file) plots[sample + '.' + exome] = plot_file for chrpos in freq_diffs[exome]: all_exome_freq_diffs[chrpos] = freq_diffs[exome][chrpos] plot_file = 'plots/loh/all_non_ref_hg19/exome_all.' + sample + '.png' input_file = 'working/loh/all_non_ref_hg19/exome_all.' + sample plot_loh(all_exome_freq_diffs, plot_file, input_file) plots[sample + '.exome_all'] = plot_file return plots
def mk_cnv_seq_input_runner(): """Construct CNV-seq input from all_non_ref_hg19 5 paired samples""" full_data_dir = 'all_non_ref_hg19/' cnv_seq_dir = 'working/cnv_seq/' os.system('mkdir -p ' + cnv_seq_dir) output_dir = os.path.join(cnv_seq_dir, full_data_dir) os.system('mkdir -p ' + output_dir) samples2data = call_class.get_data_for_paired_samples() coverages = call_class.get_coverages(samples2data) mk_cnv_seq_input(coverages, output_dir) sample_pairs = [] for sample in coverages: sample_pairs.append((sample + 'T', sample + 'N')) return sample_pairs