stringdb_alias

A python package for working with string-db.org aliases (gene and protein ID mapping).

This package is specifically for working offline using downloaded files. For accessing the STRINGdb API instead, see for example the stringdb package.

Usage

Mapping HGNC symbols

First, download the aliases and info files from string-db.org:

$ wget https://stringdb-static.org/download/protein.info.v11.5/9606.protein.info.v11.5.txt.gz
$ wget https://stringdb-static.org/download/protein.aliases.v11.5/9606.protein.aliases.v11.5.txt.gz

Then, initialize our mapper object with the downloaded files, and map lists of IDs

from stringdb_alias import HGNCMapper

mapper = HGNCMapper('9606.protein.info.v11.5.txt.gz', '9606.protein.aliases.v11.5.txt.gz')

print(mapper.get_string_ids(['ADCK2', 'TOMM7', 'PRODH']))

The mapper always returns a pandas Series. This is convenient for directly mapping a column in a DataFrame. Moreover, if the input list is a pandas Series, the index is preserved in the output.