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Bio::AlignIO::largemulUsersContributed Perl DoBio::AlignIO::largemultifasta(3)

NAME
       Bio::AlignIO::largemultifasta - Largemultifasta 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
       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.

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://github.com/bioperl/bioperl-live/issues

AUTHORS	- Albert Vilella, Heikki Lehvaslaiho
       Email: avilella-at-gmail-dot-com, 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_seq
	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

   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 largemultifasta format
	Returns	: 1 for	success	and 0 for error
	Args	: L<Bio::Align::AlignI>	object

perl v5.32.1			  2019-12-07  Bio::AlignIO::largemultifasta(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHORS - Albert Vilella, Heikki Lehvaslaiho | APPENDIX

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