How to use the pyensembl.EnsemblRelease function in pyensembl

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github openvax / pyensembl / test / test_release_versions.py View on Github external
def test_version_too_old_47():
    EnsemblRelease(47)
github openvax / pyensembl / test / test_attributes.py View on Github external
from pyensembl import EnsemblRelease

ensembl75 = EnsemblRelease(75)


def test_gene_ids():
    # only load chromosome 1 to speed up tests
    df = ensembl75.dataframe(contig="1")
    assert 'gene_id' in df
    # Ensembl gene ids are formatted like ENSG00000223972
    # which is always length 15
    assert (df['gene_id'].str.len() == 15).all(), \
        df[df['gene_id'].str.len() != 15]
github openvax / pyensembl / test / test_release_versions.py View on Github external
def test_version_is_not_numeric():
    EnsemblRelease("wuzzle")
github openvax / pyensembl / test / test_release_versions.py View on Github external
def test_version_is_none():
    EnsemblRelease(None)
github murphycj / AGFusion / agfusion / cli.py View on Github external
# if user does not specify a sqlite database then use the one provided
    # by the package

    db_file = split(args.database)[1]
    species = db_file.split('.')[1]
    release = db_file.split('.')[2]

    assert species in AVAILABLE_ENSEMBL_SPECIES, 'unsupported species!'

    agfusion_db = agfusion.AGFusionDB(args.database, debug=args.debug)
    agfusion_db.build = species + '_' + str(release)

    # get the pyensembl data

    pyensembl_data = pyensembl.EnsemblRelease(release, species)

    try:
        pyensembl_data.db
    except ValueError:
        agfusion_db.logger.error(
            "Missing pyensembl data. Run pyensembl install --release " +
            "{} --species {}".format(release, species)
        )
        exit()

    # parse the re-coloring and re-naming

    colors = {}
    rename = {}

    if args.rename is not None:
github openvax / varcode / varcode / filter_coding_variants.py View on Github external
parser = argparse.ArgumentParser()

parser.add_argument("input",
    help="VCF input file")

parser.add_argument("--output-vcf",
    help="VCF output file (keeping only header and coding variants)")

parser.add_argument("--output-csv",
    help="CSV output with chr/pos/ref/alt from VCF and annotation")


if __name__ == "__main__":
    # TODO: determine ensembl release from VCF metadata
    ensembl = pyensembl.EnsemblRelease(75)

    args = parser.parse_args()
    with open(args.input, 'r') as f:
        vcf_reader = vcf.Reader(f)
        for record in vcf_reader:
            chrom, pos = record.CHROM, record.POS
            ref, alt = record.REF, record.ALT
            gene_names =  ensembl.gene_names_at_locus(chrom, pos)
            print chrom, "@", pos, " :: ", ref, "->", alt
            for gene in gene_names:
                print "  ", gene
                # TODO: implement transcript_names_of_gene_name in pyensembl
                # and transcript_name_of_transcript_id
                transcript_ids = ensembl.transcript_ids_of_gene_name(gene)
                for transcript_id in transcript_ids:
                    print "    ", transcript_id
github openvax / varcode / varcode / variant_annotator.py View on Github external
def __init__(self, ensembl_release):
        self.ensembl = pyensembl.EnsemblRelease(ensembl_release)