MakeBlastDb: Create a BLAST Database from R
In npcooley/SynExtend: Tools for Comparative Genomics

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`	Character; Either `'prot'` for amino acid input, `'nucl'` for nucleotide input, or an unambiguous abbreviation.
`dbname`	Character; Name of the resulting database. If not provided, defaults to a random string prefixed by `blastdb`.
`dbpath`	Character; Path where database should be created. If not provided, defaults to `TMPDIR`.
`extraArgs`	Character; Additional arguments to be passed to the query executed on the command line. This should be a single string.
`createDirectory`	Logical; Determines if a directory should be created for the database if it doesn't already exist. If `FALSE`, the function will throw an error instead of creating a directory.
`verbose`	Logical; Determines if status messages should be displayed while running.

Details

MakeBlastDb is a barebones wrapper for makeblastdb from the BLAST+ commandline tools. It is set up for convenience purposes only and does not add any additional functionality. Requires a functioning installation of the BLAST+ commandline tools.