Trim void ranks in lineages

Usage

trim_void(lineage, same = TRUE, only_tail = FALSE)

Arguments

lineage: string. Vector of lineages.
same: logical. Does the lineage have the same depth? Default to TRUE.
only_tail: Logical. If FALSE (default), void ranks amid lineages and subranks are removed. If TRUE, only final void ranks are removed.

Value

The trimmed lineages. Depth could be different among them.

Details

If there is a void rank amid a lineage, deeper ranks will be removed. See the example with lineage3.

Examples

lineage1 <- "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__|f__"
lineage2 <- "k__Bacteria|p__Firmicutes|c__"
lineage3 <- "k__Bacteria|p__|c__Verrucomicrobiae|o__|f__"
trim_void(c(lineage1, lineage2, lineage3), same = FALSE)
#> [1] "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
#> [2] "k__Bacteria|p__Firmicutes"                         
#> [3] "k__Bacteria"                                       
trim_void(c(lineage1, lineage2, lineage3), same = FALSE, only_tail = TRUE)
#> [1] "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
#> [2] "k__Bacteria|p__Firmicutes"                         
#> [3] "k__Bacteria|p__|c__Verrucomicrobiae"