iskandr
commented
1 year ago 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)})
DDudka9
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