Python export_theta示例

示例#1

文件： theta.py 项目： jpmtavares/bcbio-nextgen

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

示例#2

文件： theta.py 项目： hjanime/bcbio-nextgen

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)

示例#3

文件： theta.py 项目： elkingtonmcb/bcbio-nextgen

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)

示例#4

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)