NAME

Bio::AlignIO::fasta - FastA 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 fasta flat file databases. This is for the fasta sequence format NOT FastA analysis program. To process the pairwise alignments from a FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module.

FEEDBACK

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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/

AUTHORS - Peter Schattner

Email: schattner@alum.mit.edu

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