IDswapper

Convert given gene IDs to various other IDs. (under development, please come back later)

Usage
$ IDswapper --infile test.txt --id-column-index 0 --fetch "25" "5" "10" --outfile append_test.txt

For large files that are gzip compressed
$ IDswapper --infile test.tsv.gz --id-column-index 0 --fetch "25" "5" "10" --outfile append_test.tsv.gz

The --id-column-index allows query by picking any column in large files with many columns

Fetch Table
These are the options supported for the --fetch argument
More options will be released in the next update

Example

1. Input file

2. Execute idswapper tool

$ IDswapper --infile test.txt --id-column-index 0 --fetch "25" "5" "10" --outfile append_test.txt

3. Output file

INSTALLATION
$ pip install IDswapper

Create the local idswapper database

requires mysql up and running
you can check using $ systemctl mysql status
Next,

$ python3 setup_db.py
Make sure the entries match the mysql db configuration filedb_config.json