patpat 1.0.0

Patpat is public proteomics dataset search framework that only requires protein identifiers to be passed in to search for relevant datasets.

Patpat

Patpat is public proteomics dataset search framework that only requires protein identifiers to be passed in to search for relevant datasets

Base Usage

Load Patpat package and create runtime environment:

import patpat.hub as hub
import patpat.mapper as mapper
import patpat.utility as utility

utility.init()
utility.initiate_uniprot_proteome_catalog()

Directory structure of the runtime environment is as follows:

patpat_env/
    |-- logs/
    |-- tmp/
    |-- result/
    |-- proteome/
        |-- UP_README_yyyy-mm-dd

Get the search configs via the QueryHub:

identifier_ = 'P23950'
q = hub.QueryHub()
q.identifier = identifier_
q.simple_query()

conf_ = q.get_query_config()

Set up Mappers for MapperHub, search and get results:

mappers_ = [mapper.PrideMapper(), mapper.IProXMapper()]

m = hub.MapperHub(config=conf_,
                  mappers=mappers_,
                  )
m.mapping()

result_ = m.export()

Result files store in patpat_envs/result/<task_uuid>, you can find <task_uuid> by m.config

In its current version, Patpat supports both PRIDE and iProX databases. In addition, Patpat is an extensible framework and users are encouraged to extend it with databases of interest to Patpat or to build their processes.

For more information, see GitHub (https://github.com/henry-leo/Patpat).