def _add_scatter_plot(out, data):
out_file = "%s-scatter.pdf" % os.path.splitext(out["cnr"])[0]
priority_regions = dd.get_priority_regions(data)
if not priority_regions:
return None
priority_bed = plot._prioritize_plot_regions(pybedtools.BedTool(priority_regions), data)
if utils.file_exists(out_file):
return out_file
cnr = _remove_haplotype_chroms(out["cnr"], data)
cns = _remove_haplotype_chroms(out["cns"], data)
with file_transaction(data, out_file) as tx_out_file:
cmd = [_get_cmd(), "scatter", "-s", cns, "-o", tx_out_file, "-l", priority_bed, cnr]
do.run(cmd, "CNVkit scatter plot")
return out_file
def _add_scatter_plot(out, data):
out_file = "%s-scatter.pdf" % os.path.splitext(out["cnr"])[0]
priority_bed = dd.get_svprioritize(data)
if not priority_bed:
return None
priority_bed = plot._prioritize_plot_regions(pybedtools.BedTool(priority_bed), data, os.path.dirname(out_file))
if utils.file_exists(out_file):
return out_file
cnr = _remove_haplotype_chroms(out["cnr"], data)
cns = _remove_haplotype_chroms(out["cns"], data)
with file_transaction(data, out_file) as tx_out_file:
cmd = [_get_cmd(), "scatter", "-s", cns, "-o", tx_out_file, "-l",
priority_bed, cnr]
do.run(_prep_cmd(cmd, tx_out_file), "CNVkit scatter plot")
return out_file
def _add_scatter_plot(out, data):
out_file = os.path.join(_sv_workdir(data),
os.path.splitext(os.path.basename(out["cnr"]))[0] + "-scatter.pdf")
priority_bed = dd.get_svprioritize(data)
if not priority_bed:
return None
priority_bed = plot._prioritize_plot_regions(pybedtools.BedTool(priority_bed), data, os.path.dirname(out_file))
if utils.file_exists(out_file):
return out_file
cnr = _remove_haplotype_chroms(out["cnr"], data)
cns = _remove_haplotype_chroms(out["cns"], data)
with file_transaction(data, out_file) as tx_out_file:
cmd = [_get_cmd(), "scatter", "-s", cns, "-o", tx_out_file, "-l",
priority_bed, cnr]
do.run(_prep_cmd(cmd, tx_out_file), "CNVkit scatter plot")
return out_file
