bio::alignio::metafasta(3pm) [debian man page]

Bio::AlignIO::metafasta(3pm)				User Contributed Perl Documentation			      Bio::AlignIO::metafasta(3pm)

NAME

       Bio::AlignIO::metafasta - Metafasta MSA Sequence input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::AlignIO class.

DESCRIPTION

       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.

SEE ALSO

       Bio::SeqIO::metafasta

FEEDBACK

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       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.

   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:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Heikki Lehvaslaiho
       Email heikki-at-bioperl-dot-org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   next_aln
	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

   write_aln
	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

   width
	Title	: width
	Usage	: $obj->width($newval)
	Function: Get/Set the line width for METAFASTA output
	Returns : value of width
	Args	: newvalue (optional)

perl v5.14.2							    2012-03-02					      Bio::AlignIO::metafasta(3pm)

Check Out this Related Man Page

Bio::AlignIO::psi(3pm)					User Contributed Perl Documentation				    Bio::AlignIO::psi(3pm)

NAME

       Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files

SYNOPSIS

       This module will parse PSI-BLAST output of the format seqid XXXX

DESCRIPTION

       This is a parser for psi-blast blocks.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       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.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::AlignIO::psi->new();
	Function: Builds a new Bio::AlignIO::psi object
	Returns : Bio::AlignIO::psi
	Args	:

   next_aln
	Title	: next_aln
	Usage	: $aln = $stream->next_aln()
	Function: returns the next alignment in the stream
	Returns : Bio::Align::AlignI object
	Args	: NONE

       See Bio::Align::AlignI

   write_aln
	Title	: write_aln
	Usage	: $stream->write_aln(@aln)
	Function: writes the NCBI psi-format object (.aln) into the stream
	Returns : 1 for success and 0 for error
	Args	: Bio::Align::AlignI object

       Bio::Align::AlignI

perl v5.14.2							    2012-03-02						    Bio::AlignIO::psi(3pm)

Linux and UNIX Man Pages

bio::alignio::metafasta(3pm) [debian man page]

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