bio::alignio::selex(3pm) [debian man page]
Bio::AlignIO::selex(3pm) User Contributed Perl Documentation Bio::AlignIO::selex(3pm) NAME
Bio::AlignIO::selex - selex sequence input/output stream SYNOPSIS
# Do not use this module directly. Use it via the L<Bio::AlignIO> class. use Bio::AlignIO; use strict; my $in = Bio::AlignIO->new(-format => 'selex', -file => 't/data/testaln.selex'); while( my $aln = $in->next_aln ) { } DESCRIPTION
This object can transform Bio::Align::AlignI objects to and from selex flat file databases. 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 - Peter Schattner Email: schattner@alum.mit.edu CONTRIBUTORS
Jason Stajich, jason-at-bioperl.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. Tries to read *all* selex It reads all non whitespace characters in the alignment area. For selexs with weird gaps (eg ~~~) map them by using $al->map_chars('~','-') Returns : L<Bio::Align::AlignI> object Args : NONE write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in selex format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object perl v5.14.2 2012-03-02 Bio::AlignIO::selex(3pm)
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Bio::AlignIO::nexml(3pm) User Contributed Perl Documentation Bio::AlignIO::nexml(3pm) NAME
Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver 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 NeXML format. For more information on NeXML, visit <http://www.nexml.org>. 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
Chase Miller CONTRIBUTORS
Mark Jensen, maj@fortinbras.us Rutger Vos, rutgeraldo@gmail.com 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 : Bio::Align::AlignI object - returns 0 on end of file or on error Args : See Bio::Align::AlignI rewind Title : rewind Usage : $alnio->rewind Function: Resets the stream Returns : none Args : none doc Title : doc Usage : $treeio->doc Function: Returns the biophylo nexml document object Returns : Bio::Phylo::Project Args : none or Bio::Phylo::Project object write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in nexml format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object See Bio::Align::AlignI perl v5.14.2 2012-03-02 Bio::AlignIO::nexml(3pm)