The umgap prot2kmer command takes one or more peptides as input and outputs all their k-length subsequences in order of appearance.

Usage

The input is given in a FASTA format on standard input with a single peptide per FASTA header, which may be hardwrapped with newlines. All overlapping k-mers of a peptide are written to standard output, separated by newlines. The k-mer length is configurable with the -k option, and is 9 by default.

$ cat input.fa
>header1
DAIGDVAKAYKKAG*S
$ umgap prot2kmer < input.fa
>header1
DAIGDVAKA
AIGDVAKAY
IGDVAKAYK
GDVAKAYKK
DVAKAYKKA
VAKAYKKAG
AKAYKKAG*
KAYKKAG*S
-h / --help
Prints help information
-V / --version
Prints version information
-k / --length k
The k-mer length [default: 9]