Convert given gene IDs to various other IDs.
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
| Entries | 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