NAME

Bio::Phylo::Parsers::Taxlist - Parser used by Bio::Phylo::IO, no serviceable parts inside inside.

DESCRIPTION

This module is used for importing sets of taxa from plain text files, one taxon on each line. It is called by the Bio::Phylo::IO object, so look there for usage examples. If you want to parse from a string, you may need to indicate the field separator (default is '\n') to the Bio::Phylo::IO->parse call:

 -fieldsep => '\n',

INHERITED METHODS

Bio::Phylo::Parsers::Taxlist inherits from one or more superclasses. This means that objects of class Bio::Phylo::Parsers::Taxlist also "do" the methods from the superclasses in addition to the ones implemented in this class. Below is the documentation for those additional methods, organized by superclass.

SUPERCLASS Bio::Phylo::IO

Bio::Phylo::Parsers::Taxlist inherits from superclass Bio::Phylo::IO. Below are the public methods (if any) from this superclass.

parse()

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.          

unparse()

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)

SEE ALSO

Bio::Phylo::IO

The taxon list parser is called by the Bio::Phylo::IO object. Look there for examples.

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.

REVISION

 $Id: Taxlist.pm 843 2009-03-04 23:50:27Z rvos $