Python create_path_if_nonexistent示例

示例#1

    def run(self):
        brca_resources_dir = self.cfg.resources_dir
        artifacts_dir = pipeline_utils.create_path_if_nonexistent(
            self.cfg.output_dir + "/release/artifacts")

        os.chdir(gnomAD_method_dir)

        args = [
            "python", "gnomad_to_vcf.py", "-i",
            self.input().path, "-o",
            self.output().path, "-a", "gnomADAnnotation", "-r",
            brca_resources_dir + "/refseq_annotation.hg19.gp", "-g",
            brca_resources_dir + "/hg19.fa", "-l",
            artifacts_dir + "/gnomAD_error_variants.log", "-s", "gnomAD"
        ]

        logger.info("Running gnomad_to_vcf.py with the following args: %s",
                    args)

        sp = subprocess.Popen(args,
                              stdout=subprocess.PIPE,
                              stderr=subprocess.PIPE)
        pipeline_utils.print_subprocess_output_and_error(sp)

        pipeline_utils.check_file_for_contents(self.output().path)

示例#2

    def run(self):
        artifacts_dir = pipeline_utils.create_path_if_nonexistent(
            self.cfg.output_dir + "/release/artifacts")
        os.chdir(gnomAD_method_dir)

        args = [
            "python", "download_gnomad_data.py", "-o",
            self.output().path, "-l",
            artifacts_dir + "/download_gnomAD_data.log"
        ]
        sp = subprocess.Popen(args,
                              stdout=subprocess.PIPE,
                              stderr=subprocess.PIPE)

        pipeline_utils.print_subprocess_output_and_error(sp)

        pipeline_utils.check_file_for_contents(self.output().path)

示例#3

    def __init__(self, *args, **kwargs):
        super(GnomADTask, self).__init__(*args, **kwargs)
        self.gnomAD_file_dir = self.cfg.file_parent_dir + "/gnomAD"
        self.gnomAD_static_file = "gnomAD.concatted.clean.tsv"

        pipeline_utils.create_path_if_nonexistent(self.gnomAD_file_dir)

示例#4

文件： esp_processing.py 项目： pawelciesielka/brca-exchange

    def __init__(self, *args, **kwargs):
        super(ESPTask, self).__init__(*args, **kwargs)
        self.esp_file_dir = self.cfg.file_parent_dir + "/ESP"
        self.esp_tar_file_name = esp_data_url.split('/')[-1]

        pipeline_utils.create_path_if_nonexistent(self.esp_file_dir)

示例#5

文件： pipeline_common.py 项目： BD2KGenomics/brca-exchange

    def run(self):
        pipeline_utils.create_path_if_nonexistent(
            os.path.dirname(self.output().path))

        copy(self.req_task.output().path, self.output().path)
        pipeline_utils.check_file_for_contents(self.output().path)

示例#6

文件： esp_processing.py 项目： BD2KGenomics/brca-exchange

    def __init__(self, *args, **kwargs):
        super(ESPTask, self).__init__(*args, **kwargs)
        self.esp_file_dir = self.cfg.file_parent_dir + "/ESP"
        self.esp_tar_file_name = esp_data_url.split('/')[-1]

        pipeline_utils.create_path_if_nonexistent(self.esp_file_dir)

示例#7

文件： pipeline_common.py 项目： jcasalet/brca-exchange

    def run(self):
        pipeline_utils.create_path_if_nonexistent(
            os.path.dirname(self.output().path))

        copy(self.req_task.output().path, self.output().path)
        pipeline_utils.check_file_for_contents(self.output().path)

示例#8

    def __init__(self, *args, **kwargs):
        super(GnomADTask, self).__init__(*args, **kwargs)
        self.gnomAD_file_dir = self.cfg.file_parent_dir + "/gnomAD"
        self.gnomAD_download_file_name = "gnomAD.tsv"

        pipeline_utils.create_path_if_nonexistent(self.gnomAD_file_dir)