How to use the genomepy.genome.Genome function in genomepy

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github vanheeringen-lab / genomepy / genomepy / functions.py View on Github external
def generate_exports():
    """Print export commands for setting environment variables."""
    env = []
    for name in list_installed_genomes():
        try:
            g = Genome(name)
            env_name = re.sub(r"[^\w]+", "_", name).upper()
            env.append(f"export {env_name}={g.filename}")
        except FastaIndexingError:
            pass
    return env
github vanheeringen-lab / genomepy / genomepy / genome.py View on Github external
def __init__(self, name, genomes_dir=None):
        self.genomes_dir = get_genomes_dir(genomes_dir, check_exist=False)
        self.name = self._parse_name(name)
        self.filename = self._parse_filename(name)
        super(Genome, self).__init__(self.filename)

        # file paths
        self.genome_file = self.filename
        self.genome_dir = os.path.dirname(self.filename)
        self.index_file = self.filename + ".fai"
        self.sizes_file = self.genome_file + ".sizes"
        self.gaps_file = os.path.join(self.genome_dir, self.name + ".gaps.bed")
        self.readme_file = os.path.join(self.genome_dir, "README.txt")

        # genome attributes
        self.sizes = {}
        self.gaps = {}
        metadata = self._read_metadata()
        self.tax_id = metadata.get("tax_id")
        self.assembly_accession = metadata.get("assembly_accession")
github vanheeringen-lab / genomepy / genomepy / functions.py View on Github external
mask=mask,
            regex=regex,
            invert_match=invert_match,
            localname=localname,
            bgzip=bgzip,
            **kwargs,
        )
        genome_found = True

        # Export installed genome(s)
        generate_env()

    # Generates a Fasta object, index, gaps and sizes file
    g = None
    if genome_found:
        g = Genome(localname, genomes_dir=genomes_dir)

    # Check if any annotation flags are given, if annotation already exists, or if downloading is forced
    if any(
        [
            annotation,
            only_annotation,
            skip_sanitizing,
            kwargs.get("to_annotation"),
            kwargs.get("ucsc_annotation_type"),
        ]
    ):
        annotation = True
    annotation_found = len(glob_ext_files(out_dir, "gtf")) >= 1
    if (not annotation_found or force) and annotation:
        # Download annotation from provider
        p = ProviderBase.create(provider)