Bio::Phylo::Parsers - A library for parsing phylogenetic data files and strings
my $parser = new Bio::Phylo::Parsers; $parser->parse(-file => 'data.nex', -format => 'Nexus');
The Bio::Phylo::Parsers object is the unified 'front door' for parsing trees, lists of taxa and data matrices. It imports the appropriate subclass at runtime based on the '-format' argument.
Type : Constructor Title : new Usage : my $parser = new Bio::Phylo::Parsers; Function: Initializes a Bio::Phylo::Parsers object. Returns : A Bio::Phylo::Parsers object. Args : none.
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 can either parse from_handle, i.e. from a file handle that gets passed to them, or from_string (i.e. from a scalar). I can see this expand to include the capability to parse from a database handle, and perhaps from a URL.
Type : Parsers Title : parse(%options) Usage : $parser->parse(%options); Function: Creates (file) handle, instantiates appropriate parser. Returns : L<Phylo> object Args : -file => (path), -string => (scalar), -format => (description format), -other => (parser specific options)
Rutger Vos, <rvosa@sfu.ca> http://www.sfu.ca/~rvosa/
<rvosa@sfu.ca>
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.
bug-bio-phylo@rt.cpan.org
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 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.