SYNOPSISDo not use this module directly. Use it via the Bio::AlignIO class.
DESCRIPTIONThis object can transform Bio::SimpleAlign objects to and from largemultifasta 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.
Reimplementation of Bio::AlignIO::fasta modules so that creates temporary files instead of keeping the whole sequences in memory.
SupportPlease direct usage questions or support issues to the mailing list:
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 BugsReport 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:
AUTHORS - Albert Vilella, Heikki LehvaslaihoEmail: avilella-at-gmail-dot-com, heikki-at-bioperl-dot-org
APPENDIXThe rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream while taking care of the length Returns : Bio::Seq object Args : NONE
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 largemultifasta format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object