Python package to convert between various gene or protein IDs
This is the first package I am releasing into the wild. Any feedback would be greatly appreciated! I hope this project can be used as an example for beginners on how to structure/code a simple bioinformatics tool.
I created this package because I needed a simple tool to convert between the multitude of IDs used to identify genes, proteins, etc... This is important because databases hosted by various scientific institutions (NIH, EMBL, etc) sometimes have different nomenclature to describe the same exact thing(gene, protein, dna, rna, etc).
Reddit: <https://www.reddit.com/r/bioinformatics/comments/4icres/new_bioinformatics_python_package_to_easily/>
$ pip install --upgrade pyEntrezId
from PyEntrezId import Conversion
EnsemblId = 'ENST00000407559'
# include your email address
Id = Conversion('dummyemail@dummybunny.info')
EntrezId = Id.convert_ensembl_to_entrez(EnsemblId)
# Returns a string
print(EntrezId)
from PyEntrezId import Conversion
# HGNCID can be just the number or 'HGNC:9425'
HGNCID = 9245
# include your email address
Id = Conversion('dummyemail@dummybunny.info')
EntrezId = Id.convert_hgnc_to_entrez(HGNCID)
# Returns a dictionary containing Symbol and Entrez Id
print EntrezID
from PyEntrezId import Conversion
EntrezID = 39
# include your email address
Id = Conversion('dummyemail@dummybunny.info')
UniProtId = Id.convert_entrez_to_uniprot(EntrezID)
# Returns a string
print UniProtId
from PyEntrezId import Conversion
UniProtId = 'Q9BWD1'
# include your email address
Id = Conversion('dummyemail@dummybunny.info')
EntrezID = Id.convert_uniprot_to_entrez(UniProtId)
# Returns a string
print EntrezID
from PyEntrezId import Conversion
AccessionId = 'AC131209'
# include your email address
Id = Conversion('dummyemail@dummybunny.info')
TaxID = Id.convert_accesion_to_taxid(AccesionId)
# Returns a string
print TaxID
from PyEntrezId import Conversion
# HGNCID can be just the number or 'HGNC:9425'
Symbol = 'CDK2'
# include your email address
Id = Conversion('dummyemail@dummybunny.info')
EntrezId = Id.convert_symbol_to_entrezid(Symbol)
# Returns a dictionary containing Symbol and Entrez Id
print EntrezID
Contributions to this library are always welcome and highly encouraged.
See CONTRIBUTING for more information on how to get started.
The MIT License (MIT) - See LICENSE for more information.