pyEntrezId 1.5.8

Converts UniProt, HGNC, and Ensembl Transcript Ids to Entrez Gene Id. Also, converts accession number to Taxonomy id

Python package to convert between various gene or protein IDs

Summary

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).

Links to Discussion

Reddit: <https://www.reddit.com/r/bioinformatics/comments/4icres/new_bioinformatics_python_package_to_easily/>

Quick Start

$ pip install --upgrade pyEntrezId

Examples

Convert Ensemble Transcript Gene Id to Entrez Gene Id

from PyEntrezId import Conversion

EnsemblId = 'ENST00000407559'
# include your email address
Id = Conversion('[e-mail]')
EntrezId = Id.convert_ensembl_to_entrez(EnsemblId)
# Returns a string
print(EntrezId)

Convert HGNC ID to Entrez Gene Id

from PyEntrezId import Conversion

# HGNCID can be just the number or 'HGNC:9425'
HGNCID = 9245
# include your email address
Id = Conversion('[e-mail]')
EntrezId = Id.convert_hgnc_to_entrez(HGNCID)
# Returns a dictionary containing Symbol and Entrez Id
print EntrezID

Convert Entrez Gene Id to Uniprot ID

from PyEntrezId import Conversion

EntrezID = 39
# include your email address
Id = Conversion('[e-mail]')
UniProtId = Id.convert_entrez_to_uniprot(EntrezID)
# Returns a string
print UniProtId

Convert Uniprot Id to Entrez Gene Id

from PyEntrezId import Conversion

UniProtId = 'Q9BWD1'
# include your email address
Id = Conversion('[e-mail]')
EntrezID = Id.convert_uniprot_to_entrez(UniProtId)
# Returns a string
print EntrezID

Convert Accession Id to Taxonomy Id

from PyEntrezId import Conversion

AccessionId = 'AC131209'
# include your email address
Id = Conversion('[e-mail]')
TaxID = Id.convert_accesion_to_taxid(AccesionId)
# Returns a string
print TaxID

Contributing

Contributions to this library are always welcome and highly encouraged.

See CONTRIBUTING for more information on how to get started.

License

The MIT License (MIT) - See LICENSE for more information.