def draw_coverage_histograms(coverage_dict, contigs_fpaths, output_dirpath):
total_len = dict()
contigs_dict = dict()
contigs_with_coverage = [contigs_fpath for contigs_fpath in contigs_fpaths if coverage_dict[contigs_fpath]]
for contigs_fpath in contigs_fpaths:
total_len[contigs_fpath] = reporting.get(contigs_fpath).get_field(reporting.Fields.TOTALLEN)
contigs_dict[contigs_fpath] = reporting.get(contigs_fpath).get_field(reporting.Fields.CONTIGS)
cov_values = [coverage_dict[contigs_fpath] for contigs_fpath in contigs_with_coverage]
num_contigs = [contigs_dict[contigs_fpath] for contigs_fpath in contigs_with_coverage]
common_coverage_values, bin_size, low_threshold, high_threshold, max_cov = binning_coverage(cov_values, num_contigs)
histogram_title = 'Coverage histogram (bin size: ' + str(bin_size) + 'x)'
plotter.coverage_histogram(contigs_with_coverage, common_coverage_values, output_dirpath + '/coverage_histogram',
histogram_title, bin_size=bin_size, max_cov=max_cov, low_threshold=low_threshold, high_threshold=high_threshold)
for contigs_fpath in contigs_with_coverage:
coverage_values, bin_size, low_threshold, high_threshold, max_cov = binning_coverage([coverage_dict[contigs_fpath]],
[contigs_dict[contigs_fpath]])
label = qutils.label_from_fpath(contigs_fpath)
corr_label = qutils.label_from_fpath_for_fname(contigs_fpath)
histogram_title = label + ' coverage histogram (bin size: ' + str(bin_size) + 'x)'
histogram_fpath = os.path.join(output_dirpath, corr_label + '_coverage_histogram')
plotter.coverage_histogram([contigs_fpath], coverage_values, histogram_fpath,
histogram_title, draw_bars=True, bin_size=bin_size, max_cov=max_cov,
low_threshold=low_threshold, high_threshold=high_threshold)
def draw_coverage_histograms(coverage_dict, contigs_fpaths, output_dirpath):
total_len = dict()
contigs_dict = dict()
contigs_with_coverage = [contigs_fpath for contigs_fpath in contigs_fpaths if coverage_dict[contigs_fpath]]
for contigs_fpath in contigs_fpaths:
total_len[contigs_fpath] = reporting.get(contigs_fpath).get_field(reporting.Fields.TOTALLEN)
contigs_dict[contigs_fpath] = reporting.get(contigs_fpath).get_field(reporting.Fields.CONTIGS)
cov_values = [coverage_dict[contigs_fpath] for contigs_fpath in contigs_with_coverage]
num_contigs = [contigs_dict[contigs_fpath] for contigs_fpath in contigs_with_coverage]
common_coverage_values, bin_size, low_threshold, high_threshold, max_cov = binning_coverage(cov_values, num_contigs)
histogram_title = 'Coverage histogram (bin size: ' + str(bin_size) + 'x)'
plotter.coverage_histogram(contigs_with_coverage, common_coverage_values, output_dirpath + '/coverage_histogram',
histogram_title, bin_size=bin_size, max_cov=max_cov, low_threshold=low_threshold, high_threshold=high_threshold)
for contigs_fpath in contigs_with_coverage:
coverage_values, bin_size, low_threshold, high_threshold, max_cov = binning_coverage([coverage_dict[contigs_fpath]],
[contigs_dict[contigs_fpath]])
label = qutils.label_from_fpath(contigs_fpath)
corr_label = qutils.label_from_fpath_for_fname(contigs_fpath)
histogram_title = label + ' coverage histogram (bin size: ' + str(bin_size) + 'x)'
histogram_fpath = os.path.join(output_dirpath, corr_label + '_coverage_histogram')
plotter.coverage_histogram([contigs_fpath], coverage_values, histogram_fpath,
histogram_title, draw_bars=True, bin_size=bin_size, max_cov=max_cov,
low_threshold=low_threshold, high_threshold=high_threshold)