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.\" ========================================================================
.\"
.IX Title "Bio::SeqIO::metafasta 3pm"
.TH Bio::SeqIO::metafasta 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::SeqIO::metafasta \- metafasta sequence input/output stream
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Do not use this module directly.  Use it via the Bio::SeqIO class.
.PP
.Vb 1
\&  use Bio::SeqIO;
\&
\&  # read the metafasta file
\&  $io = Bio::SeqIO\->new(\-file => "test.metafasta",
\&                        \-format => "metafasta" );
\&
\&  $seq = $io\->next_seq;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object can transform Bio::Seq::Meta objects to and from metafasta
flat file databases.
.PP
For sequence part the code is an exact copy of Bio::SeqIO::fasta
module. The only added bits deal with meta data \s-1IO.\s0
.PP
The format of a metafasta file is
.PP
.Vb 6
\&  >test
\&  ABCDEFHIJKLMNOPQRSTUVWXYZ
\&  &charge
\&  NBNAANCNJCNNNONNCNNUNNXNZ
\&  &chemical
\&  LBSAARCLJCLSMOIMCHHULRXRZ
.Ve
.PP
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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Heikki Lehvaslaiho"
.IX Header "AUTHOR - Heikki Lehvaslaiho"
Email heikki-at-bioperl-dot-org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "next_seq"
.IX Subsection "next_seq"
.Vb 5
\& Title   : next_seq
\& Usage   : $seq = $stream\->next_seq()
\& Function: returns the next sequence in the stream
\& Returns : Bio::Seq object
\& Args    : NONE
.Ve
.SS "write_seq"
.IX Subsection "write_seq"
.Vb 5
\& Title   : write_seq
\& Usage   : $stream\->write_seq(@seq)
\& Function: writes the $seq object into the stream
\& Returns : 1 for success and 0 for error
\& Args    : array of 1 to n Bio::PrimarySeqI objects
.Ve
.SS "width"
.IX Subsection "width"
.Vb 5
\& Title   : width
\& Usage   : $obj\->width($newval)
\& Function: Get/Set the line width for METAFASTA output
\& Returns : value of width
\& Args    : newvalue (optional)
.Ve