The umgap translate command takes one or more DNA sequences and translates them into amino acid sequences.

Usage

The DNA sequences are expected in a FASTA format on standard input.

$ cat input.fa
>header1
GATTACAAA
$ umgap translate -f1 < input.fa
>header1
DYK

The -f flag allows you to add reading frames to the translation. If you want to translate multiple frames and care to keep them apart, the -n flag adds the name of the frame to the end of the FASTA header.

$ umgap translate -f1 -f1R < input.fa
>header1|1
DYK
>header1|1R
FVI

The -a flag can be used as a shortcut to translate all 6 reading frames.

With the -t flag, you can select a specific translation table, for instance -t11 for the bacterial, archaeal and plant plastid code.

-a / --all-frames
Read and output all six frames
-n / --append-name
Append a bar (|) and the name of the frame to the fasta header
-h / --help
Prints help information
-m / --methionine
Replace each start-codon with methionine
-s / --show-table
Instead of normal use, print the selected table and exit
-V / --version
Prints version information
-f / --frame f...
Adds a reading frame (1, 2, 3, 1R, 2R or 3R)
-t / --table t
Translation table to use [default: 1]