MakeBlastDb: Create a BLAST Database from R
In npcooley/SynExtend: Tools for Working With Synteny Objects

MakeBlastDb

R Documentation

Create a BLAST Database from R

Description

Wrapper to create BLAST databases for subsequent queries using the commandline BLAST tool directly from R. Can operate on an XStringSet or a FASTA file.

This function requires the BLAST+ commandline tools, which can be downloaded here.

Usage

MakeBlastDb(seqs, dbtype=c('prot', 'nucl'), 
          dbname=NULL, dbpath=NULL,
          extraArgs='', createDirectory=FALSE, 
          verbose=TRUE)

Arguments

`seqs`	Sequence(s) to create a BLAST database from. This can be either an `XStringSet` or a path to a FASTA file.
`dbtype`	Either `'prot'` for amino acid input, or `'nucl'` for nucleotide input.
`dbname`	Name of the resulting database. If not provided, defaults to a random string prefixed by `blastdb`.
`dbpath`	Path where database should be created. If not provided, defaults to `TMPDIR`.
`extraArgs`	Additional arguments to be passed to the query executed on the command line. This should be a single character string.
`createDirectory`	Should a directory be created for the database if it doesn't exist? If `FALSE`, the function will throw an error instead of creating a directory.
`verbose`	Should output be displayed?

Details

This offers a quick way to create BLAST databases from R. This function essentially wraps the makeblastdb commandline function. All arguments supported by makeblastdb are supported in the extraArgs argument.