IDswapper 0.1.8

A tool for swapping IDs in a file by fetching various IDs from idswapper database

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

Fetch Argument	Columns to be appended
2	Ensembl Transcript ID
3	Ensembl Protein ID
4	HGNC ID
5	Gene Symbol
6	Gene Description
10	Chromosome Location
12	Gene Aliases
18	Entrez Gene ID
19	Ensembl Gene ID
20	VEGA ID
21	UCSC ID
23	Refseq Accession
25	Uniprot ID
30	COSMIC Entry
31	OMIM ID
36	Orphanet ID
43	CD Name
47	RNA Central ID
51	MANE Select ID

Example

1. Input file

Entries
ENSG00000075624
ENSG00000146648
ENSG00000141510

2. Execute idswapper tool

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

3. Output file

Fetch Argument	Uniprot ID	Gene Symbol	Chromosome Location
ENSG00000075624	P60709	ACTB	7p22.1
ENSG00000146648	P00533	EGFR	7p11.2
ENSG00000141510	P04637	TP53	17p13.1

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