umgap translate
Translates a FASTA stream of DNA reads to peptides
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]