umgap splitkmers
Splits a TSV stream of peptides and taxon IDs into k-mers and taxon IDs
The umgap splitkmers command takes tab-separated taxon IDs and protein sequences and outputs
the k-mers mapped to the taxon IDs.
Usage
The input is given on standard input and should be a TSV formatted stream of taxon IDs and a protein sequence from this taxon. The output will be written to standard output and consists of a TSV formatted stream of k-mers mapped to the taxa in which they occur. The k-mer length is configurable with the -k option, and is 9 by default.
This output stream is ready to be grouped by K-mer by sorting and then aggregated into a
searchable index, with the sort, umgap joinkmers and umgap buildindex commands.
$ cat input.tsv 654924 MNAKYDTDQGVGRMLFLGTIGLAVVVGGLMAYGYYYDGKTPSSGTSFHTASPSFSSRYRY 176652 MIKLFCVLAAFISINSACQSSHQQREEFTVATYHSSSICTTYCYSNCVVASQHKGLNVESYTCDKPDPYGRETVCKCTLIKCHDI $ umgap splitkmers < input.tsv MNAKYDTDQ 654924 NAKYDTDQG 654924 AKYDTDQGV 654924 KYDTDQGVG 654924 YDTDQGVGR 654924 ... SPSFSSRYR 654924 PSFSSRYRY 654924 MIKLFCVLA 176652 IKLFCVLAA 176652 KLFCVLAAF 176652 ...
- -h / --help
- Prints help information
- -V / --version
- Prints version information
- -k / --length k
- The k-mer length [default: 9]
- -p / --prefix p
- Print only the (k-1)-mer suffixes of the k-mers starting with this character