How to use the pyensembl.species.Species.register function in pyensembl

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github rraadd88 / beditor / beditor / lib / get_seq.py View on Github external
def get_seq_aminoacid(cfg,din):
    """
    Fetches sequences if mutation format is amino acid 

    :param cfg: configuration dict
    :param din: input data
    :returns dsequences: dataframe with sequences
    """
    import pyensembl
    #import ensembl object that would fetch genes 
    # ensembl = pyensembl.EnsemblRelease(release=cfg['genomerelease'])
    ensembl = pyensembl.EnsemblRelease(species=pyensembl.species.Species.register(
    latin_name=cfg['host'],
    synonyms=[cfg['host']],
    reference_assemblies={
    cfg['genomeassembly']: (cfg['genomerelease'], cfg['genomerelease']),
    }),release=cfg['genomerelease'])
    
    din.index=range(len(din))
    dbedp='{}/dbedflank.bed'.format(cfg['datad'])
    dbed=pd.DataFrame(columns=bed_colns)
    terrpositions=[]
    terrnotfound=[]
    terrnoncoding=[]
    bedrowi=0
#             for i in trange(len(din)-1,desc='get positions for bedtools'):                
    for i in din.index:                
        if din.loc[i,'transcript: id'] in ensembl.transcript_ids():
github openvax / pyensembl / pyensembl / species.py View on Github external
mouse = Species.register(
    latin_name="mus_musculus",
    synonyms=["mouse", "house mouse"],
    reference_assemblies={
        "NCBIM37": (54, 67),
        "GRCm38": (68, MAX_ENSEMBL_RELEASE),

    })

dog = Species.register(
    latin_name="canis_familiaris",
    synonyms=["dog"],
    reference_assemblies={"CanFam3.1": (75, MAX_ENSEMBL_RELEASE)})

cat = Species.register(
    latin_name="felis_catus",
    synonyms=["cat"],
    reference_assemblies={"Felis_catus_6.2": (75, MAX_ENSEMBL_RELEASE)})

chicken = Species.register(
    latin_name="gallus_gallus",
    synonyms=["chicken"],
    reference_assemblies={
        "Galgal4": (75, 85),
        "Gallus_gallus-5.0": (86, MAX_ENSEMBL_RELEASE)})

# Does the black rat (Rattus Rattus) get used for research too?
brown_rat = Species.register(
    latin_name="rattus_norvegicus",
    synonyms=["brown rat", "lab rat", "rat"],
    reference_assemblies={
github openvax / pyensembl / pyensembl / species.py View on Github external
return Species._latin_names_to_species[latin_name]


def check_species_object(species_name_or_object):
    """
    Helper for validating user supplied species names or objects.
    """
    if isinstance(species_name_or_object, Species):
        return species_name_or_object
    elif isinstance(species_name_or_object, str):
        return find_species_by_name(species_name_or_object)
    else:
        raise ValueError("Unexpected type for species: %s : %s" % (
            species_name_or_object, type(species_name_or_object)))

human = Species.register(
    latin_name="homo_sapiens",
    synonyms=["human"],
    reference_assemblies={
        "GRCh38": (76, MAX_ENSEMBL_RELEASE),
        "GRCh37": (55, 75),
        "NCBI36": (54, 54),
    })

mouse = Species.register(
    latin_name="mus_musculus",
    synonyms=["mouse", "house mouse"],
    reference_assemblies={
        "NCBIM37": (54, 67),
        "GRCm38": (68, MAX_ENSEMBL_RELEASE),

    })
github openvax / pyensembl / pyensembl / species.py View on Github external
reference_assemblies={"CanFam3.1": (75, MAX_ENSEMBL_RELEASE)})

cat = Species.register(
    latin_name="felis_catus",
    synonyms=["cat"],
    reference_assemblies={"Felis_catus_6.2": (75, MAX_ENSEMBL_RELEASE)})

chicken = Species.register(
    latin_name="gallus_gallus",
    synonyms=["chicken"],
    reference_assemblies={
        "Galgal4": (75, 85),
        "Gallus_gallus-5.0": (86, MAX_ENSEMBL_RELEASE)})

# Does the black rat (Rattus Rattus) get used for research too?
brown_rat = Species.register(
    latin_name="rattus_norvegicus",
    synonyms=["brown rat", "lab rat", "rat"],
    reference_assemblies={
        "Rnor_5.0": (75, 79),
        "Rnor_6.0": (80, MAX_ENSEMBL_RELEASE),
    })
github openvax / pyensembl / pyensembl / species.py View on Github external
reference_assemblies={
        "GRCh38": (76, MAX_ENSEMBL_RELEASE),
        "GRCh37": (55, 75),
        "NCBI36": (54, 54),
    })

mouse = Species.register(
    latin_name="mus_musculus",
    synonyms=["mouse", "house mouse"],
    reference_assemblies={
        "NCBIM37": (54, 67),
        "GRCm38": (68, MAX_ENSEMBL_RELEASE),

    })

dog = Species.register(
    latin_name="canis_familiaris",
    synonyms=["dog"],
    reference_assemblies={"CanFam3.1": (75, MAX_ENSEMBL_RELEASE)})

cat = Species.register(
    latin_name="felis_catus",
    synonyms=["cat"],
    reference_assemblies={"Felis_catus_6.2": (75, MAX_ENSEMBL_RELEASE)})

chicken = Species.register(
    latin_name="gallus_gallus",
    synonyms=["chicken"],
    reference_assemblies={
        "Galgal4": (75, 85),
        "Gallus_gallus-5.0": (86, MAX_ENSEMBL_RELEASE)})
github openvax / pyensembl / pyensembl / species.py View on Github external
"NCBIM37": (54, 67),
        "GRCm38": (68, MAX_ENSEMBL_RELEASE),

    })

dog = Species.register(
    latin_name="canis_familiaris",
    synonyms=["dog"],
    reference_assemblies={"CanFam3.1": (75, MAX_ENSEMBL_RELEASE)})

cat = Species.register(
    latin_name="felis_catus",
    synonyms=["cat"],
    reference_assemblies={"Felis_catus_6.2": (75, MAX_ENSEMBL_RELEASE)})

chicken = Species.register(
    latin_name="gallus_gallus",
    synonyms=["chicken"],
    reference_assemblies={
        "Galgal4": (75, 85),
        "Gallus_gallus-5.0": (86, MAX_ENSEMBL_RELEASE)})

# Does the black rat (Rattus Rattus) get used for research too?
brown_rat = Species.register(
    latin_name="rattus_norvegicus",
    synonyms=["brown rat", "lab rat", "rat"],
    reference_assemblies={
        "Rnor_5.0": (75, 79),
        "Rnor_6.0": (80, MAX_ENSEMBL_RELEASE),
    })
github openvax / pyensembl / pyensembl / species.py View on Github external
elif isinstance(species_name_or_object, str):
        return find_species_by_name(species_name_or_object)
    else:
        raise ValueError("Unexpected type for species: %s : %s" % (
            species_name_or_object, type(species_name_or_object)))

human = Species.register(
    latin_name="homo_sapiens",
    synonyms=["human"],
    reference_assemblies={
        "GRCh38": (76, MAX_ENSEMBL_RELEASE),
        "GRCh37": (55, 75),
        "NCBI36": (54, 54),
    })

mouse = Species.register(
    latin_name="mus_musculus",
    synonyms=["mouse", "house mouse"],
    reference_assemblies={
        "NCBIM37": (54, 67),
        "GRCm38": (68, MAX_ENSEMBL_RELEASE),

    })

dog = Species.register(
    latin_name="canis_familiaris",
    synonyms=["dog"],
    reference_assemblies={"CanFam3.1": (75, MAX_ENSEMBL_RELEASE)})

cat = Species.register(
    latin_name="felis_catus",
    synonyms=["cat"],