NAME¶

mbfa - Murasaki Binary FASTA format converter

SYNOPSIS¶

 mbfa [options...] [input] [input2 ...] #convert [input] and [input2 ...] to Muraaski Binary FASTA files

DESCPRIPTION¶

Murasaki processes sequence data using a 2-bit format where each base is reprsented using 2 bits. There's a number of pre-existing formats that do similar things, however in particular Murasaki needs to know about the metadata that can't be expressed in just 2 bits (eg. where sequences of NNNNs are, sequence breaks when multiple sequences are included in a FASTA file, etc.), therefore the MBFA format includes this data as well. Ordinarily these files are generated automatically by Murasaki when first run on a new sequence.

Because the file format is designed mesh closely with Murasaki, the actual file extension will vary to reflect your architecture. It will generally be some form of .mbfa[48][48] (e.g. ".mbfa88" (the default gcc build on an amd64)).

OPTIONS¶

--info|-i

Show metadata about each MBFA specified.

--force|-f

By default mbfa will skip files that already have recent .mbfa files. This option forces the regeneration of these files.

--fatal|-F

Makes errors fatal. Ordinarily if you specify multiple files, mbfa will try to convert all of them even if one fails emitting a warning. With --fatal it will stop and exit with an error if there's a problem.

--fasta|-A

Geneates FASTA output corresponding based on the MBFA data to stdout.

--help|-h, --version|-V, --verbose|-V

What you'd expect.

LICENSE¶

GNU General Public License, version 3 (GPLv3)

AVAILABILITY¶

<http://murasaki.sourceforge.net>

AUTHOR¶

Kris Popendorf <krisp@dna.bio.keio.ac.jp>

SEE ALSO¶

murasaki(1), geneparse(1)