Bio::Phylo::IO - Front end for parsers and serializers
use Bio::Phylo::IO qw(parse unparse);
# returns an unblessed array reference of block objects,
# i.e. taxa, matrix or forest objects
my $blocks = parse(
'-file' => $file,
'-format' => 'nexus',
);
for my $block ( @{ $blocks } ) {
if ( $block->isa('Bio::Phylo::Taxa') ) {
my $taxa = $block;
# do something with the taxa
}
}
# returns a Bio::Phylo::Project object
my $project = parse(
'-file' => $file,
'-format' => 'nexus',
'-as_project' => 1
)
my ($taxa) = @{ $project->get_taxa };
# parsing a tree from a newick string
my $tree_string = '(((A,B),C),D);';
my $tree = Bio::Phylo::IO->parse(
'-string' => $tree_string,
'-format' => 'newick',
)->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 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 front end for parsing and serializing 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. The parse and unparse subroutines load and dispatch the appropriate sub-modules at runtime, depending on the '-format' argument.
Parses a file or string.
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)
Comments: 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.
If @ARGV contains even key/value pairs such
as "format newick file <filename>" (note: no
dashes) these will be prepended to @_, for
one-liners.
Unparses object(s) to a string.
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 and http://rutgervos.blogspot.com
$Id: IO.pm 841 2009-03-04 23:07:30Z rvos $
