umgap snaptaxon
Snaps taxon IDs to a rank or specified taxa.
The umgap snaptaxon command takes one or more taxon IDs. For each taxon, it searches amongst
its ancestors if any are of the specified rank (e.g., -r species), or are one of the listed
taxa (e.g., -t 1598 -t 1883). If so, the taxon is replaced by the most specific of these
matching taxa. Otherwise, it is mapped to the root of the taxonomy.
Usage
The input is given on standard input and may be any sequence of FASTA headers and/or lines containing a single taxon ID. The FASTA headers (if any) are just copied over to standard output.
The taxonomy to be used is passed as an argument to this command. This is a preprocessed version of the NCBI taxonomy.
$ cat input.fa >header1 888268 186802 1598 1883 $ umgap snaptaxon 2020-04-taxons.tsv -r order < ~/input.fa >header1 38820 186802 186826 85011 $ umgap snaptaxon 2020-04-taxons.tsv -t 1239 2 < ~/input.fa >header1 1 1239 1239 2
- -h / --help
- Prints help information
- -i / --invalid
- Include the invalidated taxa from the taxonomy
- -V / --version
- Prints version information
- -r / --rank r
- The rank to snap towards [possible values: superkingdom, kingdom, subkingdom, superphylum, phylum, subphylum, superclass, class, subclass, infraclass, superorder, order, suborder, infraorder, parvorder, superfamily, family, subfamily, tribe, subtribe, genus, subgenus, species group, species subgroup, species, subspecies, varietas, forma]
- -t / --taxons t...
- A taxon to snap towards (allow multiple times)