splitAlignment: Split alignments.

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

Description

Split alignments into individual files.

Usage

splitAlignment(file, output, split_by = NULL, format = "fasta",
  colw = 10000, checkAmbiguity = TRUE, checkInternalGaps = FALSE, ...)

Arguments

file	path and file name of the alignment (all the seq need to be the same length)
output	folder where the individual sequences will be stored
split_by	If NULL (default), each sequence will be a in a separate file. Otherwise, a data frame with at least 2 columns named ‘groups’ and ‘sequences’: sequences identified in the ‘sequences’ column, sharing the same values in the ‘groups’ column will be written to files.
format	format of the alignment, for now only fasta
colw	width of columns, same as in write.dna
checkAmbiguity	should the presence of ambiguities in the sequences be tested? (default=TRUE). If ambiguities are found, returns a warning.
checkInternalGaps	should the presence of internal gaps be tested? (default=FALSE). If internal gaps are found, returns a warning.
...	additional parameters to be passed to ape:::write.dna

Details

This function takes an alignment and put each sequence into its individual file that is named the same as the name of the sequence. This function also overwrites the output (it doesn't check that the file created don't already exist).

Value

TRUE if the function succeed, mostly used for its side effect (create files with individual sequences).

Author(s)

Francois Michonneau

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