How to use the pyensembl.ensembl_grch37 function in pyensembl

def test_maf():
    expected_tcga_ov_variants = [
        Variant(1, 1650797, "A", "G", ensembl),
        Variant(1, 23836447, "C", "A", ensembl),
        Variant(1, 231401797, "A", "C", ensembl),
        Variant(11, 124617502, "C", "G", ensembl),
    ]
    eq_(len(tcga_ov_variants), len(expected_tcga_ov_variants))
    for v_expect, v_maf in zip(expected_tcga_ov_variants, tcga_ov_variants):
        eq_(v_expect, v_maf)
        gene_name = tcga_ov_variants.metadata[v_maf]['Hugo_Symbol']
        assert any(gene.name == gene_name for gene in v_maf.genes), \
            "Expected gene name %s but got %s" % (gene_name, v_maf.genes)

def test_noncoding_polymorphic_pseudogene():
    # variant in MROH5-001, which is a polymorphic pseudogene
    variant = Variant("8", 142458077, "C", "T", ensembl_grch37)
    expect_effect(
        variant,
        transcript_id="ENST00000430863",
        effect_class=NoncodingTranscript,
        modifies_coding_sequence=False,
        modifies_protein_sequence=False)

def validate_transcript_mutation(
        ensembl_transcript_id,
        chrom,
        dna_position,
        dna_ref,
        dna_alt,
        aa_pos,
        aa_alt):
    variant = Variant(chrom, dna_position, dna_ref, dna_alt, ensembl_grch37)
    effects = variant.effects()
    transcript_id_dict = {
        effect.transcript.id: effect
        for effect in effects
        if isinstance(effect, TranscriptMutationEffect)
    }
    assert ensembl_transcript_id in transcript_id_dict, \
        "%s not found in %s" % (ensembl_transcript_id, transcript_id_dict)
    effect = transcript_id_dict[ensembl_transcript_id]

    if isinstance(effect, ExonicSpliceSite):
        # exonic splice site mutations carry with them an alternate effect
        # which is what we check against dbNSFP (since that database seemed
        # to ignore exonic splicing mutations)
        effect = effect.alternate_effect

def test_release_75_contig_1():
    df = ensembl_grch37.gtf.dataframe(contig="1")
    assert df is not None
    assert len(df) > 0
    assert (df.seqname == "1").all()
    df = ensembl_grch37.gtf.dataframe(contig=1)
    assert df is not None
    assert len(df) > 0
    assert (df.seqname == "1").all()

def test_maf():
    expected_tcga_ov_variants = [
        Variant(1, 1650797, "A", "G", ensembl),
        Variant(1, 23836447, "C", "A", ensembl),
        Variant(1, 231401797, "A", "C", ensembl),
        Variant(11, 124617502, "C", "G", ensembl),
    ]
    eq_(len(tcga_ov_variants), len(expected_tcga_ov_variants))
    for v_expect, v_maf in zip(expected_tcga_ov_variants, tcga_ov_variants):
        eq_(v_expect, v_maf)
        gene_name = tcga_ov_variants.metadata[v_maf]['Hugo_Symbol']
        assert any(gene.name == gene_name for gene in v_maf.genes), \
            "Expected gene name %s but got %s" % (gene_name, v_maf.genes)

def test_silent_stop_codons():
    silent_stop_codon_variants = {
        "ENST00000290524": Variant(
            contig=1,
            start=151314663,
            ref="C",
            alt="T",
            ensembl=ensembl_grch37),
        "ENST00000368725": Variant(
            contig=1,
            start=153409535,
            ref="C",
            alt="T",
            ensembl=ensembl_grch37),
        "ENST00000353479": Variant(
            contig=10,
            start=105791994,
            ref="C",
            alt="T",
            ensembl=ensembl_grch37),
    }
    for transcript_id, variant in silent_stop_codon_variants.items():
        yield (
            expect_effect,

from __future__ import absolute_import

import functools

from pyensembl import (
    ensembl_grch37,
    ensembl_grch38,
    cached_release
)
from nose.tools import nottest

major_releases = [
    ensembl_grch37,
    ensembl_grch38
]

contigs = list(range(1, 23)) + ["X", "Y", "M"]

@nottest
def test_ensembl_releases(*versions):
    """
    Run a unit test which takes an EnsemblRelease as an argument
    for multiple releases (most recent for each reference genome)
    """
    if len(versions) == 0:
        ensembl_releases = major_releases
    else:
        ensembl_releases = [cached_release(version) for version in versions]

def test_release_75_contig_MT():
    df = ensembl_grch37.gtf.dataframe(contig="M")
    assert df is not None
    assert len(df) > 0
    assert (df.seqname == "MT").all()
    df = ensembl_grch37.gtf.dataframe(contig="MT")
    assert df is not None
    assert len(df) > 0
    assert (df.seqname == "MT").all()

def _get_effect(chrom, pos, dna_ref, dna_alt, transcript_id):
    variant = Variant(chrom, pos, dna_ref, dna_alt, ensembl=ensembl)
    effects = variant.effects()
    transcript_dict = effects.top_priority_effect_per_transcript_id()
    assert transcript_id in transcript_dict, \
        "Expected transcript ID %s for variant %s not found in %s" % (
            transcript_id, variant, transcript_dict)
    effect = transcript_dict[transcript_id]

    # COSMIC seems to ignore exonic splice sites
    if isinstance(effect, ExonicSpliceSite):
        return effect.alternate_effect
    else:
        return effect