Bio::AlignIO::largemulUsersContributed Perl DoBio::AlignIO::largemultifasta(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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 v5.14.1 2011-07-22 Bio::AlignIO::largemultifasta(3)
