bio::treeio::tabtree(3pm) [debian man page]
Bio::TreeIO::tabtree(3pm) User Contributed Perl Documentation Bio::TreeIO::tabtree(3pm) NAME
Bio::TreeIO::tabtree - A simple output format which displays a tree as an ASCII drawing SYNOPSIS
use Bio::TreeIO; my $in = Bio::TreeIO->new(-file => 'input', -format => 'newick'); my $out = Bio::TreeIO->new(-file => '>output', -format => 'tabtree'); while( my $tree = $in->next_tree ) { $out->write_tree($tree); } DESCRIPTION
This is a made up format just for outputting trees as an ASCII drawing. FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists 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 of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Jason Stajich Email jason@bioperl.org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $obj = Bio::TreeIO::tabtree->new(); Function: Builds a new Bio::TreeIO::tabtree object Returns : Bio::TreeIO::tabtree Args : write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Write a tree out to data stream in newick/phylip format Returns : none Args : Bio::Tree::TreeI object next_tree Title : next_tree Usage : Function: Sorry not possible with this format Returns : none Args : none perl v5.14.2 2012-03-02 Bio::TreeIO::tabtree(3pm)
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Bio::TreeIO::nexus(3pm) User Contributed Perl Documentation Bio::TreeIO::nexus(3pm) NAME
Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP SYNOPSIS
use Bio::TreeIO; my $in = Bio::TreeIO->new(-file => 't/data/cat_tre.tre'); while( my $tree = $in->next_tree ) { } DESCRIPTION
This is a driver module for parsing PAUP Nexus tree format which basically is just a remapping of trees. Comments The nexus format allows node comments that are placed inside square brackets. Usually the comments (implemented as tags for nodes) are used to give a name for an internal node or record the bootstap value, but other uses are possible. The FigTree program by Andrew Rambaut adds various rendering parameters inside comments and flags these comments by starting them with '&!'. The parameters implemented here are 'label' and 'color'. FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists 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 of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Jason Stajich Email jason-at-open-bio-dot-org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Args : -header => boolean default is true print/do not print #NEXUS header -translate => boolean default is true print/do not print Node Id translation to a number next_tree Title : next_tree Usage : my $tree = $treeio->next_tree Function: Gets the next tree in the stream Returns : Bio::Tree::TreeI Args : none write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Writes a tree onto the stream Returns : none Args : Bio::Tree::TreeI header Title : header Usage : $obj->header($newval) Function: Example : Returns : value of header (a scalar) Args : on set, new value (a scalar or undef, optional) translate_node Title : translate_node Usage : $obj->translate_node($newval) Function: Example : Returns : value of translate_node (a scalar) Args : on set, new value (a scalar or undef, optional) perl v5.14.2 2012-03-02 Bio::TreeIO::nexus(3pm)