rPlant (version 2.16)

Mafft: MAFFT Multiple Sequence Alignment

Description

WRAPPER DEPRECATED -- one can install mafft on Agave API and use this wrapper as a prototype -- MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of about 200 sequences), FFT-NS-2 (fast; for alignment of about 10,000 sequences), etc. See http://mafft.cbrc.jp/alignment/software/. The manual is also available here: http://mafft.cbrc.jp/alignment/software/manual/manual.html

Usage

Mafft(file.name, file.path="", type="DNA", aln.filetype="FASTA", args=NULL,  out.name=NULL, print.curl=FALSE, job.name=NULL, shared.username=NULL,  suppress.Warnings=FALSE)

Arguments

file.name

name of file to be evaluated on the Discovery Environment (DE), see details for supported input formats.

file.path

optional path to a user's subdirectory on the DE; default path is empty, which leads to the home directory

type

Two options "PROTEIN" or "DNA". This defines the type of sequences in the file, either proteins or nucleotides.

aln.filetype

Mafft does alignment of sequences, this option selects the file type of that result file. There are two options FASTA and CLUSTALW

args

Optional for arguments (i.e. flags). The Mafft model has much additional functionality that is not in this wrapper function (http://mafft.cbrc.jp/alignment/software/manual/manual.html#lbAI), see details. This option allows users to add anything that is not included (.i.e. args="--auto"), which automatically selects an appropriate strategy according to data size, see details.

out.name

the name to given to the output file (default mafft.aln)

job.name

the name to give the job being submitted

print.curl

Prints the curl statement that can be used in the terminal, if curl is installed on your computer

shared.username

With iPlant you have the ability to share folders with other users. If someone has shared a folder with you and you want to run a job with them, enter their username for this input.

suppress.Warnings

This will turn off the warnings, will speed up run time. Use with caution, if the inputs are incorrect they will not be caught.

Value

A list containing the job id and the job name is provided for jobs submitted. If an error, then a message stating the error should also be reported.

Details

The supported input file format is the fasta format http://en.wikipedia.org/wiki/FASTA_format.

Additional arguments, args, can be found at http://mafft.cbrc.jp/alignment/software/manual/manual.html#lbAI. The args input is text with the flags and inputs for those flags in a string like on the command line.

There are two options for output files: FASTA http://en.wikipedia.org/wiki/FASTA_format and CLUSTALW http://meme.nbcr.net/meme/doc/clustalw-format.html. The result file is ALWAYS `mafft.aln'.

See Also

ListApps, Validate, UploadFile

Examples

## Not run: data(DNA.fasta)
## Not run: write.fasta(sequences = DNA.fasta, names = names(DNA.fasta), file.out = "DNA.fasta")
## Not run: Validate("username","password")
## Not run: UploadFile("DNA.fasta", filetype="FASTA-0")
## Not run: Mafft("DNA.fasta", job.name="MafftFASTA")