get_proteins: Retrieve protein sequences and data from GenBank and Uniprot

In fcampelo/epitopes: Processing and Feature Extraction for Epitope Data

Retrieve protein sequences and data from GenBank and Uniprot

Description

This function is used to retrieve data from Genbank's protein database for given protein IDs. If an ID is not available from Genbank the function will try to retrieve it from Uniprot.

Usage

get_proteins(uids, save_folder = NULL)

Arguments

uids	A character vector with protein IDs, or a data.table object of class LBCE_dt, generated by get_LBCE().
save_folder	path to folder for saving the results.

Details

Queries are processed one by one (rather than in batch) to enable treatment of individual inconsistencies (e.g., wrong UIDs, queries that return a different identifier, etc.). This makes this routine substantially slower, but considerably more robust to errors.

Value

A list object containing a data frame with the extracted proteins plus a vector of IDs that were not successfully retrieved.

Author(s)

Felipe Campelo ([e-mail])

fcampelo/epitopes documentation built on April 22, 2023, 12:23 a.m.