removeEmptySeqs: Remove empty sequences

In fmichonneau/chopper: Alignment Manipulations and Data Preparation for Phylogenetic Analyses

Description

Removes empty sequences from an alignment

Usage

removeEmptySeqs(file, output, formatin = "fasta", formatout = formatin,
  colsep = "", overwrite = FALSE, ...)

Arguments

file	path and file name for a DNA alignment
output	path and file name of the alignment with the missing data removed. If missing, the original file is overwritten, with an a posteriori warning, unless quiet=TRUE.
formatin	format of the alignment to check (to be passed to read.dna)
formatout	format of the alignemnt to write (to be passed to write.dna)
colsep	argument to be passed to write.dna, character used to separate columns in DNA alignment (ape's default is a single space, here we override this to no character, i.e. colsep="").
overwrite	If no output file is specified and if overwrite is TRUE, the original file is overwritten.
...	additional arguments to be passed to write.dna.

Details

This function takes an alignment, and remove sequences that only contains gaps. This function can read the same type of alignment files as ape:::read.dna, and output the same formats as ape:::write.dna

Value

TRUE if function succeedeed, but mostly used for its side effect of creating a new alignment file.

Author(s)

Francois Michonneau

fmichonneau/chopper documentation built on May 16, 2019, 1:43 p.m.