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
