fastaconc {EnvNJ}

R Documentation

Concatenate Fasta Files in a Single Multispecies Fasta File

Description

Concatenate fasta files from different species in a single multispecies fasta file.

Usage

fastaconc(otus, inputdir = ".", out.file = "./concatenated_multispecies.fasta")

Arguments

otus	a character vector giving the otus' names.
inputdir	path to the directory containing the individual fasta files.
out.file	path and name of output file.

Details

When we have fasta files (extension should be '.fasta'), each one for a species containing different sequences of the given species, this function concatenate the different sequences of the same species and writes it as a single sequence in a single multispecies fasta file. If the individual fasta files are found in the working directory, the inputdir argument don't need to be passed. The names of the individual fasta files must match the otus' names.

Value

A single multispecies fasta file with the sequences of each species spliced in a single sequence.

See Also

df2fasta()

Examples

## Not run: fastaconc(otus = c('Glis_glis', 'Ovis_aries', 'Sus_scrofa'))

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