umgap taxa2freq
Counts ranked taxon occurrences in a stream of taxon IDs or arguments.
The umgap taxa2freq command creates a frequency table of a list of taxa on a given target rank
(species by default). When invoked with file arguments, it adds a column for each file.
Usage
The input is given on standard input, or in multiple file arguments, a single taxon ID on each line. Each taxon that is more specific than the target rank is counted towards its ancestor on the target rank. Each taxon less specific than the target rank is counted towards root. The command outputs a CSV table of counts, taxon IDs and their names.
The taxonomy to be used is passed as an argument to this command. This is a preprocessed version of the NCBI taxonomy.
$ cat input.txt 9606 9606 2759 9606 9606 9606 9606 9606 9606 9606 8287 $ umgap taxa2freq taxons.tsv < input.txt taxon id,taxon name,stdin 1,root,2 9606,Homo sapiens,9 $ umgap taxa2freq taxons.tsv input.txt input.txt taxon id,taxon name,input.txt,input.txt 1,root,2,2 9606,Homo sapiens,9,9
With the -r option, the default species rank can be set to any named rank.
$ umgap taxa2freq -r phylum taxons.tsv < input.txt taxon id,taxon name,stdin 7711,Chordata,10
- -h / --help
- Prints help information
- -V / --version
- Prints version information
- -f / --frequency f
- The minimum frequency to be reported [default: 1]
- -r / --rank r
- The rank to show [default: species]