Python plot_multiple_regions_coverage Examples

Example #1

File: plot.py Project: zengfengbo/bcbio-nextgen

def by_regions(items):
    """Plot for a union set of combined ensemble regions across all of the data
       items.
    """
    work_dir = os.path.join(dd.get_work_dir(items[0]), "structural", "coverage")
    safe_makedir(work_dir)
    out_file = os.path.join(work_dir, "%s-coverage.pdf" % (dd.get_sample_name(items[0])))
    if file_exists(out_file):
        items = _add_regional_coverage_plot(items, out_file)
    else:
        bed_files = _get_ensemble_bed_files(items)
        merged = bed.merge(bed_files)
        breakpoints = breakpoints_by_caller(bed_files)
        if merged:
            priority_merged = _prioritize_plot_regions(merged, items[0])
            out_file = plot_multiple_regions_coverage(items, out_file, items[0], priority_merged, breakpoints)
            items = _add_regional_coverage_plot(items, out_file)
    return items

Example #2

def by_regions(items):
    """Plot for a union set of combined ensemble regions across all of the data
       items.
    """
    work_dir = os.path.join(dd.get_work_dir(items[0]), "structural", "coverage")
    safe_makedir(work_dir)
    out_file = os.path.join(work_dir, "%s-coverage.pdf" % (dd.get_sample_name(items[0])))
    if file_exists(out_file):
        items = _add_regional_coverage_plot(items, out_file)
    else:
        bed_files = _get_ensemble_bed_files(items)
        merged = bed.merge(bed_files)
        breakpoints = breakpoints_by_caller(bed_files)
        if merged:
            priority_merged = _prioritize_plot_regions(merged, items[0])
            out_file = plot_multiple_regions_coverage(items, out_file,
                                                      priority_merged, breakpoints)
            items = _add_regional_coverage_plot(items, out_file)
    return items