umgap joinkmers
Aggregates a TSV stream of peptides and taxon IDs.
The umgap joinkmers command takes tab-separated peptides and taxon IDs, aggregates the taxon
IDs where consecutive peptides are equal and outputs a tab-separated triple of peptide, consensus
taxon ID and taxon rank.
Usage
The input is given on standard input. If it is sorted on the first column, a complete mapping
from strings to aggregated taxa and its rank will be written to standard output. It is
meant to be used after the umgap splitkmers and sort commands, and it's output is ideal for umgap buildindex, but there may be further uses.
The aggregation strategy used in this command to find a consensus taxon is the hybrid approach
of the umgap taxa2agg command, with a 95% factor. This keeps the result close to the lowest
common ancestor, but filters out some outlying taxa.
The taxonomy to be used is passed as an argument to this command. This is a preprocessed version of the NCBI taxonomy.
$ cat input.tsv AAAAA 34924 AAAAA 30423 AAAAA 5678 BBBBBB 48890 BBBBBB 156563 $ umgap joinkmers taxons.tsv < input.tsv AAAAA 2759 superkingdom BBBBBB 9153 family
- -h / --help
- Prints help information
- -V / --version
- Prints version information