How to use the genomepy.provider function in genomepy

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github vanheeringen-lab / genomepy / tests / test_02_links.py View on Github external
def test_ensembl_genome_download_links():
    """Test Ensembl links for various genomes

    These genomes are hosted on ftp.ensembl.org

    Vertebrates are downloaded from HTTPS.
    """
    p = genomepy.provider.ProviderBase.create("Ensembl")

    # Only test on vertebrates as these are downloaded over HTTPS.
    # All others are downloaded over FTP, which is unreliable on Travis.
    for genome in ["Anan_2.0", "ASM303372v1"]:
        p.get_genome_download_link(genome)
github vanheeringen-lab / genomepy / tests / test_04_download_annotation.py View on Github external
def test_ensembl_annotation(localname=None):
    """Test Ensembl annotation

    This annotation is hosted on https://ftp.ensembl.org.
    """
    tmp = mkdtemp()
    p = genomepy.provider.ProviderBase.create("Ensembl")

    # Only test on vertebrates as these are downloaded over HTTPS.
    # All others are downloaded over FTP, which is unreliable on Travis.
    for name, version in [("KH", 98)]:
        p.download_annotation(name, tmp, localname=localname, version=version)

        localname = genomepy.utils.get_localname(name, localname)
        gtf = os.path.join(tmp, localname, localname + ".annotation.gtf.gz")
        validate_gzipped_gtf(gtf)

        bed = os.path.join(tmp, localname, localname + ".annotation.bed.gz")
        validate_gzipped_bed(bed)

    shutil.rmtree(tmp)
github vanheeringen-lab / genomepy / tests / test_genomepy.py View on Github external
def test_ensemblgenomes_genome_download_links():
    """Test Ensembl FTP links for various genomes

    These genomes are hosted on ftp.ensemblgenomes.org.
    """
    p = genomepy.provider.ProviderBase.create("Ensembl")

    for genome in ["AgamP4", "WBcel235", "R64-1-1"]:
        p.get_genome_download_link(genome)
github vanheeringen-lab / genomepy / tests / test_02_links.py View on Github external
def test_ensembl_download_options(assembly, masking, release_version):
    """Test masking, as well as Ensembl specific options for assembly level and release versions"""
    p = genomepy.provider.ProviderBase.create("Ensembl")

    mask = masking
    toplevel = False if assembly == "primary_assembly" else True
    version = release_version

    p.get_genome_download_link(
        "GRCh38.p13", mask=mask, toplevel=toplevel, version=version
    )
github vanheeringen-lab / genomepy / tests / test_04_download_annotation.py View on Github external
def test_UCSC_annotation(localname=None):
    """Test UCSC annotation"""
    tmp = mkdtemp()
    p = genomepy.provider.ProviderBase.create("UCSC")
    name = "sacCer3"

    p.download_annotation(name, tmp, localname=localname)

    localname = genomepy.utils.get_localname(name, localname)
    gtf = os.path.join(tmp, localname, localname + ".annotation.gtf.gz")
    validate_gzipped_gtf(gtf)

    bed = os.path.join(tmp, localname, localname + ".annotation.bed.gz")
    validate_gzipped_bed(bed)

    shutil.rmtree(tmp)