Bio::AlignIO::metafasta - Metafasta MSA Sequence input/output stream
Do not use this module directly. Use it via the Bio::AlignIO class.
This object can transform Bio::SimpleAlign objects to and from metafasta flat
file databases.
The format of a metafasta file is
>test/1-25
ABCDEFHIJKLMNOPQRSTUVWXYZ
&charge
NBNAANCNJCNNNONNCNNUNNXNZ
&chemical
LBSAARCLJCLSMOIMCHHULRXRZ
where the sequence block is followed by one or several meta blocks. Each meta
block starts with the ampersand character '&' in the first column and is
immediately followed by the name of the meta data which continues until the
new line. The meta data follows it. All characters, except new line, are
important in meta data.
Bio::SeqIO::metafasta
Please direct usage questions or support issues to the mailing list:
[email protected]
rather than to the module maintainer directly. Many experienced and reponsive
experts will be able look at the problem and quickly address it. Please
include a thorough description of the problem with code and data examples if
at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs
and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
Email heikki-at-bioperl-dot-org
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream.
Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
or on error
Args : NONE
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in fasta format
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
Title : width
Usage : $obj->width($newval)
Function: Get/Set the line width for METAFASTA output
Returns : value of width
Args : newvalue (optional)