Command line function - cds2aa

oggmap cds2aa -h

usage: oggmap <sub-command> cds2aa [-h] [-i I] [-o O] [-t T] [-r R]

options:
  -h, --help  show this help message and exit
  -i I        specify fasta input file
  -o O        specify output file [optional]
  -t T        transtable [default: std]
  -r R        specify CDS source to retain longest isoform

cds2aa example:

    # to get CDS from Danio rerio on Linux run:
    $ wget https://ftp.ensembl.org/pub/release-105/fasta/danio_rerio/cds/Danio_rerio.GRCz11.cds.all.fa.gz
    $ gunzip Danio_rerio.GRCz11.cds.all.fa.gz

    # on Mac:
    $ curl https://ftp.ensembl.org/pub/release-105/fasta/danio_rerio/cds/Danio_rerio.GRCz11.cds.all.fa.gz --remote-name
    $ gunzip Danio_rerio.GRCz11.cds.all.fa.gz

    # translate and retain longest isoform from CDS fasta file:
    $ cds2aa -i Danio_rerio.GRCz11.cds.all.fa -r ENSEMBL -o Danio_rerio.GRCz11.aa.all.longest.fa