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Refget CLI

CLI is beta and may change

The CLI is just a beta and may change at any time.

Refget also provides a command-line interface.

Computing digests

You can also use the CLI to compute to digest locally from a fasta file. 

refget digest-fasta test_fasta/base.fa -level 0
INFO:refget.refget:Digesting fasta file: test_fasta/base.fa
XZlrcEGi6mlopZ2uD8ObHkQB1d0oDwKk

refget digest-fasta test_fasta/base.fa --level 1
INFO:refget.refget:Digesting fasta file: test_fasta/base.fa
{
  "names": "Fw1r9eRxfOZD98KKrhlYQNEdSRHoVxAG",
  "sequences": "0uDQVLuHaOZi1u76LjV__yrVUIz9Bwhr"
}

use --level 2 to get the canonical representation of the sequence collection.

Adding sequence collections

Use refget add-fasta to add fasta files to the database. First you have to set the environment variables. You can run

source deployment/local_demo/local_demo.env

Or set them manually.

export POSTGRES_HOST=`pass databio/seqcol/postgres_host`
export POSTGRES_DB=`pass databio/seqcol/postgres_db`
export POSTGRES_USER=`pass databio/seqcol/postgres_user`
export POSTGRES_PASSWORD=`pass databio/seqcol/postgres_password`
export POSTGRES_TABLE="seqcol"

Then you just run

refget add-fasta -f path/to/fasta/file.fa.gz

Adding a PEP

If you have a lot of fasta files, you can add them all at the same time like

refget add-fasta -p path/to/pep.csv

This CSV file should have these columns:

  • sample_name: uniquee identifier for this fasta file
  • fasta: path to fasta file