Bio::AlignIO::fasta - FastA 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 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.
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/
Email: schattner@alum.mit.edu
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
