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('[email protected]')
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('[email protected]')
EntrezId = Id.convert_hgnc_to_entrez(HGNCID)
# Returns a dictionary containing Symbol and Entrez Id
print EntrezIDfrom PyEntrezId import Conversion
EntrezID = 39
# include your email address
Id = Conversion('[email protected]')
UniProtId = Id.convert_entrez_to_uniprot(EntrezID)
# Returns a string
print UniProtIdfrom PyEntrezId import Conversion
UniProtId = 'Q9BWD1'
# include your email address
Id = Conversion('[email protected]')
EntrezID = Id.convert_uniprot_to_entrez(UniProtId)
# Returns a string
print EntrezIDfrom PyEntrezId import Conversion
AccessionId = 'AC131209'
# include your email address
Id = Conversion('[email protected]')
TaxID = Id.convert_accesion_to_taxid(AccesionId)
# Returns a string
print TaxIDfrom PyEntrezId import Conversion
# HGNCID can be just the number or 'HGNC:9425'
Symbol = 'CDK2'
# include your email address
Id = Conversion('[email protected]')
EntrezId = Id.convert_symbol_to_entrezid(Symbol)
# Returns a dictionary containing Symbol and Entrez Id
print EntrezIDContributions 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.