uniprot-meta-tool 0.2.0

retrieves and parses metadata from UniProt.org with simple object-based interface

Uniprot meta tool

this tool is designed to be useful and simple interface for UniProt.org knowlege base witch can be used to simply get protein metadata by its ID

NOTE: this package is in early stage of development so be careful!

installation

as simple as possible:

pip install uniprot-meta-tool

only dependencies are requests and jmespath

Examples

from uniprot_meta_tool import UniprotData

>>>up_data = UniprotData('P05067')
>>>up_data.name
'Amyloid-beta precursor protein'
>>>up_data.genes[0]
'APP'
>>>up_data.organism.common_name
'Human'

some util functions are also available:

get_molecular_functions(uniprot_data) -> List[str]:
returns list of molecular functions from keywords. accepts uniprot_id as string or UniprotData object

get_biological_processes(uniprot_data) -> List[str]:
returns list of biological processes from keywords.

get_pathways(uniprot_data: UniprotData) -> List[str]:
returns list of pathways (from Reactome DB using UniProt cross-reference)    

utility to enrich dataframes (requires Pandas to be installed):

from uniprot_meta_tool.dataframe import enrich_df

df = enrich_df(
    df, # pandas DataFrame
    'protein_id', # name of column contains UniProt ID
    ['gene', 'protein_name', 'organism'] # list of parameters that should be added
)

Raw search

You can reach raw metadata from UniprotData(u_id).raw_data property.

You can use JMESPath query language to get something from raw data using UniprotData(u_id).search() method

Configuration

You can set up basic parameters of how uniprot_meta_tool works with remote API and local storage, but be careful with this

from uniprot_meta_tool.data_parser import set_config
set_config(
    meta_cache_dir='/your/local/folder', # default is %tmp%/uniprot_meta
    use_cache=True, # if you set it to False, module will not store retrieved info to your disk 
    #                 and will perform new HTTP request every time you create UniprotData object
    uniprot_rest_url='https://rest.uniprot.org/uniprotkb/{}' # have no idea why you could want to change it, but you can
)

MR and feature requests

Feel free to suggest features using GitHub issues and to implement something you need if you want to!