Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::PopGen::IO::phase - A parser for Phase format data


       # Do not use directly, use through the Bio::PopGen::IO driver

         use Bio::PopGen::IO;
         my $io = Bio::PopGen::IO->new(-format => 'phase',
                                      -file   => 'data.phase');

         # Some IO might support reading in a population at a time

         my @population;
         while( my $ind = $io->next_individual ) {
             push @population, $ind;


       A driver module for Bio::PopGen::IO for parsing phase data.

       PHASE is defined in


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AUTHOR - Rich Dobson



       Jason Stajich,


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : my $obj = Bio::PopGen::IO::hapmap->new();
        Function: Builds a new Bio::PopGen::IO::hapmap object
        Returns : an instance of Bio::PopGen::IO::hapmap
        Args    : [optional, these are the current defaults]
                  -field_delimiter => ' '
                  -allele_delimiter=> '\s+'
                  -no_header       => 0,

        Title   : flag
        Usage   : $obj->flag($flagname,$newval)
        Function: Get/Set the flag value
        Returns : value of a flag (a boolean)
        Args    : A flag name, currently we expect
                  'no_header', 'field_delimiter', or 'allele_delimiter'
                  on set, new value (a boolean or undef, optional)

        Title   : next_individual
        Usage   : my $ind = $popgenio->next_individual;
        Function: Retrieve the next individual from a dataset
        Returns : L<Bio::PopGen::IndividualI> object
        Args    : none

        Title   : next_population
        Usage   : my $ind = $popgenio->next_population;
        Function: Retrieve the next population from a dataset
        Returns : L<Bio::PopGen::PopulationI> object
        Args    : none
        Note    : Many implementation will not implement this

        Title   : write_individual
        Usage   : $popgenio->write_individual($ind);
        Function: Write an individual out in the file format
        Returns : none
        Args    : L<Bio::PopGen::PopulationI> object(s)

        Title   : write_population
        Usage   : $popgenio->write_population($pop);
        Function: Write a population out in the file format
        Returns : none
        Args    : L<Bio::PopGen::PopulationI> object(s)
        Note    : Many implementation will not implement this