branch_list2qiime: Branch list to QIIME format

In larssnip/microclass: Tools for taxonomic classification of prokaryotes

Branch list to QIIME format

Description

Creates QIIME formatted texts from a branch list.

Usage

branch_list2qiime(branch.lst)

Arguments

branch.lst

a list of branches.

Details

A QIIME formatted branch is a text with the format

"d__domain;p__phylum;c__class;o__order;f__family;g__genus;s__species"

where the words domain, phylum, etc are replaced by taxon names. This function converts a list of N branches to N such texts.

NOTE 1: This is only meaningful if the branch.lst contains names instead of tax_id's, see branch_taxid2name.

NOTE 2: The ranks are fixed to the ones listed above, where domain is the same as superkingdom in the NCBI taxonomy.

Value

The vector of texts, one for each element in branch.lst.

Author(s)

Lars Snipen.

larssnip/microclass documentation built on Nov. 1, 2023, 2:39 p.m.