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

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

NAME
Bio::AlignIO::nexus - NEXUS format sequence input/output stream SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class. use Bio::AlignIO; my $in = Bio::AlignIO->new(-format => 'nexus', -file => 'aln.nexus'); while( my $aln = $in->next_aln ) { # do something with the alignment } DESCRIPTION
This object can transform Bio::Align::AlignI objects to and from NEXUS data blocks. See method documentation for supported NEXUS features. ACKNOWLEDGEMENTS
Will Fisher has written an excellent standalone NEXUS format parser in Perl, readnexus. A number of tricks were adapted from it. 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 - 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 _ new Title : new Usage : $alignio = Bio::AlignIO->new(-format => 'nexus', -file => 'filename'); Function: returns a new Bio::AlignIO object to handle clustalw files Returns : Bio::AlignIO::clustalw object Args : -verbose => verbosity setting (-1,0,1,2) -file => name of file to read in or with ">" - writeout -fh => alternative to -file param - provide a filehandle to read from/write to -format => type of Alignment Format to process or produce Customization of nexus flavor output -show_symbols => print the symbols="ATGC" in the data definition (MrBayes does not like this) boolean [default is 1] -show_endblock => print an 'endblock;' at the end of the data (MyBayes does not like this) boolean [default is 1] next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: Returns the next alignment in the stream. Supports the following NEXUS format features: - The file has to start with '#NEXUS' - Reads in the name of the alignment from a comment (anything after 'TITLE: ') . - Sequence names can be given in a taxa block, too. - If matchchar notation is used, converts them back to sequence characters. - Does character conversions specified in the NEXUS equate command. - Sequence names of type 'Homo sapiens' and Homo_sapiens are treated identically. Returns : L<Bio::Align::AlignI> object Args : write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: Writes the $aln object into the stream in interleaved NEXUS format. Everything is written into a data block. SimpleAlign methods match_char, missing_char and gap_char must be set if you want to see them in the output. Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object flag Title : flag Usage : $obj->flag($name,$value) Function: Get/Set a flag value Returns : value of flag (a scalar) Args : on set, new value (a scalar or undef, optional) perl v5.14.2 2012-03-02 Bio::AlignIO::nexus(3pm)

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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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