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bio::alignio::largemultifasta(3pm) [debian man page]

Bio::AlignIO::largemultifasta(3pm)			User Contributed Perl Documentation			Bio::AlignIO::largemultifasta(3pm)

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://redmine.open-bio.org/projects/bioperl/ 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 v5.14.2 2012-03-02 Bio::AlignIO::largemultifasta(3pm)

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Bio::AlignIO::metafasta(3pm)				User Contributed Perl Documentation			      Bio::AlignIO::metafasta(3pm)

NAME
Bio::AlignIO::metafasta - Metafasta 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 metafasta flat file databases. The format of a metafasta file is >test/1-25 ABCDEFHIJKLMNOPQRSTUVWXYZ &charge NBNAANCNJCNNNONNCNNUNNXNZ &chemical LBSAARCLJCLSMOIMCHHULRXRZ where the sequence block is followed by one or several meta blocks. Each meta block starts with the ampersand character '&' in the first column and is immediately followed by the name of the meta data which continues until the new line. The meta data follows it. All characters, except new line, are important in meta data. SEE ALSO
Bio::SeqIO::metafasta 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://redmine.open-bio.org/projects/bioperl/ AUTHOR - Heikki Lehvaslaiho Email 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_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 width Title : width Usage : $obj->width($newval) Function: Get/Set the line width for METAFASTA output Returns : value of width Args : newvalue (optional) perl v5.14.2 2012-03-02 Bio::AlignIO::metafasta(3pm)
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