removeEmptySeqs: Remove empty sequences

Description Usage Arguments Details Value Author(s)

Description

Removes empty sequences from an alignment

Usage

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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.