g2p_mapper_cli

g2p_mapper_cli

Map positions on the genome to the protein and vice versa. Outputs a large JSON file with the "ID" field from the GFF column 9 to create keys in a mapping object

CLI usage

npm install g2p_mapper_cli
export PATH=${PATH}:./node_modules/.bin/ ## May not be required for all installs
g2pmapper --in yourfile.gff --out outDir

## will create outDir if none exists

Output

The script outputs one JSON file per transcript from the inputted GFF. The JSON files look like this

e.g. XM_047436352.2.json

{
  "g2p": { "123": 0, "124": 0, "125": 0, "126": 1, "127": 1 },
  "p2g": { "0": 123, "1": 126 },
  "strand": 1,
  "refName": "chr1"
}

• g2p gives the protein position given a genome position as a key
• p2g gives the genome position given the protein position as a key
• strand is the transcript strand
• refName is the chromosome name of the transcript

The number of files is fairly large e.g. the human GFF outputs 144000 files