pyEntrezId 1.5.5

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 created this package because there is a lack of simple developer tools to convert between the numerous 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).

There is an need to be able to perform these conversions quickly. Since I last checked, current python tools like biopython lack a complete solution to this issue.

Quick Start

$ pip install --upgrade pyEntrezId

Examples

Convert Ensemble Transcript Gene Id to Entrez Gene Id

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

Convert HGNC ID to Entrez Gene Id

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

Convert Entrez Gene Id to Uniprot ID

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

Convert Uniprot Id to Entrez Gene Id

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

Convert Accession Id to Taxonomy Id

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

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.