Splits a FASTA stream of peptides into k-mers.
umgap prot2kmer command takes one or more peptides as input and outputs all their k-length
subsequences in order of appearance.
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]