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)