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Available assemblies #257

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DDudka9 opened this issue Nov 4, 2021 · 7 comments
Closed

Available assemblies #257

DDudka9 opened this issue Nov 4, 2021 · 7 comments

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@DDudka9
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DDudka9 commented Nov 4, 2021 •
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I am quite intensely using pyensembl (mouse and human) in my molecular evolution analysis (thanks a lot to everyone working on it!). I would like to know if a chimpanzee (or any non-human assembly) will be available in the future. I also have been using the brown rat assembly and it has been working well so far - should I expect it to have more bugs than mouse or human assemblies?

Thank you for working on pyensembl,

Damian
@iskandr
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iskandr commented Feb 13, 2023

Hi Damian,

Sorry for the two years delayed response -- PyEnsembl supports a subset of the ensembl.org assemblies. Here's the current supported set:


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, 102),
        "GRCm39": (103, 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, 90),
        "Felis_catus_8.0": (91, 92),
        "Felis_catus_9.0": (93, 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, 104),
        "mRatBN7.2": (105, MAX_ENSEMBL_RELEASE)
    })

macaque = Species.register(
    latin_name="macaca_fascicularis",
    synonyms=["macaque", "Crab-eating macaque"],
    reference_assemblies={
        "Macaca_fascicularis_6.0": (103, MAX_ENSEMBL_RELEASE),
    })

green_monkey = Species.register(
    latin_name="chlorocebus_sabaeus",
    synonyms=["green_monkey", "african_green_monkey"],
    reference_assemblies={
        "ChlSab1.1": (86, MAX_ENSEMBL_RELEASE),
    })

rhesus = Species.register(
    latin_name="macaca_mulatta",
    synonyms=["rhesus"],
    reference_assemblies={"Mmul_10": (75, MAX_ENSEMBL_RELEASE)})

rabbit = Species.register(
    latin_name="oryctolagus_cuniculus",
    synonyms=["rabbit"],
    reference_assemblies={"OryCun2.0": (75, MAX_ENSEMBL_RELEASE)})

gerbil = Species.register(
    latin_name="meriones_unguiculatus",
    synonyms=["gerbil"],
    reference_assemblies={"MunDraft-v1.0": (75, MAX_ENSEMBL_RELEASE)})

syrian_hamster = Species.register(
    latin_name="mesocricetus_auratus",
    synonyms=["syrian_hamster"],
    reference_assemblies={"MesAur1.0": (75, MAX_ENSEMBL_RELEASE)})

chinese_hamster = Species.register(
    latin_name="cricetulus_griseus_chok1gshd",
    synonyms=["chinese_hamster"],
    reference_assemblies={"CHOK1GS_HDv1": (75, MAX_ENSEMBL_RELEASE)})

naked_mole_rat = Species.register(
    latin_name="heterocephalus_glaber_female",
    synonyms=["naked_mole_rat"],
    reference_assemblies={"HetGla_female_1.0": (75, MAX_ENSEMBL_RELEASE)})

guinea_pig = Species.register(
    latin_name="cavia_porcellus",
    synonyms=["guinea_pig"],
    reference_assemblies={"Cavpor3.0": (75, MAX_ENSEMBL_RELEASE)})

pig = Species.register(
    latin_name="sus_scrofa",
    synonyms=["pig"],
    reference_assemblies={"Sscrofa11.1": (75, MAX_ENSEMBL_RELEASE)})

@iskandr iskandr closed this as completed Feb 13, 2023
@iskandr
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iskandr commented Feb 13, 2023

If you're still interested, btw, I can add chimpanzee!

@DDudka9
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DDudka9 commented Feb 14, 2023 via email

@iskandr
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iskandr commented Feb 15, 2023

How's this?

https://github.com/openvax/pyensembl/pull/282/files#diff-fb115395175caaa3bb84deab38ce96cf45e60a4882a2cb34b9d7eaf117819d0dR267

@DDudka9
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DDudka9 commented Feb 15, 2023 via email

@DDudka9
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DDudka9 commented Feb 26, 2023 via email

@iskandr
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iskandr commented Feb 26, 2023 via email

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