mbfa - Online in the Cloud

PROGRAM:

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.

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