Bio::Phylo::IO - Input and output of phylogenetic data.
use Bio::Phylo::IO; # parsing a tree from a newick string my $tree_string = '(((A,B),C),D);'; my $tree = Bio::Phylo::IO->parse( '-string' => $tree_string, # old parser, always adds node labels '-format' => 'newick', )->first; # OR: $tree = Bio::Phylo::IO->parse( '-string' => $tree_string, # faster, new parser, node labels optional '-format' => 'fastnewick', # with node labels '-label' => 1, )->first; # note: newick parsers return # 'Bio::Phylo::Forest'! Call # ->first to retrieve the first # tree of the forest. # prints 'Bio::Phylo::Forest::Tree' print ref $tree, "\n"; # parsing a table my $table_string = qq(A,1,2|B,1,2|C,2,2|D,2,1); my $matrix = Bio::Phylo::IO->parse( '-string' => $table_string, '-format' => 'table', # Data type, see Bio::Phylo::Parsers::Table '-type' => 'STANDARD', # field separator '-fieldsep' => ',', # line separator '-linesep' => '|' ); # prints 'Bio::Phylo::Matrices::Matrix' print ref $matrix, "\n"; # parsing a list of taxa my $taxa_string = 'A:B:C:D'; my $taxa = Bio::Phylo::IO->parse( '-string' => $taxa_string, '-format' => 'taxlist', '-fieldsep' => ':' ); # prints 'Bio::Phylo::Taxa' print ref $taxa, "\n"; # matches taxon names in tree to $taxa object $tree->cross_reference($taxa); # likewise for matrix $matrix->cross_reference($taxa); print Bio::Phylo::IO->unparse( # pass the tree object, # crossreferenced to taxa, which # are crossreferenced to the matrix '-phylo' => $tree, '-format' => 'pagel' ); # prints a pagel data file: #4 2 #A,n1,0.000000,1,2 #B,n1,0.000000,1,2 #n1,n2,0.000000 #C,n2,0.000000,2,2 #n2,n3,0.000000 #D,n3,0.000000,2,1
The IO module is the unified front end for parsing and unparsing phylogenetic data objects. It is a non-OO module that optionally exports the 'parse' and 'unparse' subroutines into the caller's namespace, using the use Bio::Phylo::IO qw(parse unparse); directive. Alternatively, you can call the subroutines as class methods, as in the synopsis. The parse and unparse subroutines load and dispatch the appropriate sub-modules at runtime, depending on the '-format' argument.
use Bio::Phylo::IO qw(parse unparse);
parse
unparse
The parse method makes assumptions about the capabilities of Bio::Phylo::Parsers::* modules: i) their names match those of the -format => (blah) arguments, insofar that ucfirst(blah) . '.pm' is an existing module; ii) the modules implement a _from_handle, or a _from_string method. Exceptions are thrown if either assumption is violated.
Type : Class method Title : parse Usage : my $obj = Bio::Phylo::IO->parse(%options); Function: Creates (file) handle, instantiates appropriate parser. Returns : A Bio::Phylo::* object Args : -file => (path), or -string => (scalar), -format => (description format), -(other) => (parser specific options)
Type : Class method Title : unparse Usage : my $string = Bio::Phylo::IO->unparse( %options ); Function: Turns Bio::Phylo object into a string according to specified format. Returns : SCALAR Args : -phylo => (Bio::Phylo object), -format => (description format), -(other) => (parser specific options)
Also see the manual: Bio::Phylo::Manual.
CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo
Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:
bug-bio-phylo@rt.cpan.org
$Id: IO.pm 2196 2006-09-07 21:35:47Z rvosa $
Rutger A. Vos,
rvosa@sfu.ca
The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.
Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.