def run(cnv_info, somatic_info):
"""Run THetA analysis given output from CNV caller on a tumor/normal pair.
"""
cmd = _get_cmd("RunTHeTA.py")
if not cmd:
logger.info("THetA scripts not found in current PATH. Skipping.")
return cnv_info
else:
work_dir = _sv_workdir(somatic_info.tumor_data)
cnv_info = cnvkit.export_theta(cnv_info, somatic_info.tumor_data)
cnv_info = _run_theta(cnv_info, somatic_info.tumor_data, work_dir)
return cnv_info
def run(vrn_info, cnvs_by_name, somatic_info):
"""Run THetA analysis given output from CNV caller on a tumor/normal pair.
"""
cmd = _get_cmd("RunTHeTA.py")
if not cmd:
logger.info("THetA scripts not found in current PATH. Skipping.")
else:
from bcbio.structural import cnvkit
work_dir = _sv_workdir(somatic_info.tumor_data)
assert "cnvkit" in cnvs_by_name, "THetA requires CNVkit calls"
cnv_info = cnvkit.export_theta(cnvs_by_name["cnvkit"], somatic_info.tumor_data)
return _run_theta(cnv_info, somatic_info.tumor_data, work_dir)
def run(vrn_info, cnvs_by_name, somatic_info):
"""Run THetA analysis given output from CNV caller on a tumor/normal pair.
"""
cmd = _get_cmd("RunTHeTA.py")
if not cmd:
logger.info("THetA scripts not found in current PATH. Skipping.")
else:
work_dir = _sv_workdir(somatic_info.tumor_data)
assert "cnvkit" in cnvs_by_name, "THetA requires CNVkit calls"
cnv_info = cnvkit.export_theta(cnvs_by_name["cnvkit"], somatic_info.tumor_data)
cnv_info["theta_input"] = subset_by_supported(cnv_info["theta_input"], _theta_to_coords,
cnvs_by_name, work_dir, somatic_info.tumor_data)
return _run_theta(cnv_info, somatic_info.tumor_data, work_dir, run_n3=False)
def run(vrn_info, cnvs_by_name, somatic_info):
"""Run THetA analysis given output from CNV caller on a tumor/normal pair.
"""
cmd = _get_cmd("RunTHeTA.py")
if not cmd:
logger.info("THetA scripts not found in current PATH. Skipping.")
else:
work_dir = _sv_workdir(somatic_info.tumor_data)
assert "cnvkit" in cnvs_by_name, "THetA requires CNVkit calls"
cnv_info = cnvkit.export_theta(cnvs_by_name["cnvkit"], somatic_info.tumor_data)
cnv_info["theta_input"] = subset_by_supported(cnv_info["theta_input"], _theta_to_coords,
cnvs_by_name, work_dir, somatic_info.tumor_data)
return _run_theta(cnv_info, somatic_info.tumor_data, work_dir, run_n3=False)
