NAME

       Bio::PopGen::IO::prettybase - Extract individual allele data from PrettyBase format

SYNOPSIS

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

DESCRIPTION

       This object will parse comma delimited PrettyBase output.  PrettyBase is defined by the
       SeattleSNPs http://pga.gs.washington.edu/

       This is expected to be tab delimited (you can vary with the field_delimiter flag SITE
       SAMPLE ALLELE1 ALLELE2

       There are 2 initialization parameters, the delimiter (-field_delimiter) [default 'tab']
       and a boolean -no_header which specifies if there is no header line to read in.  All lines
       starting with '#' will be skipped

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

       Email jason-at-bioperl.org

CONTRIBUTORS

       Matthew Hahn, matthew.hahn-at-duke.edu

APPENDIX

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

   new
        Title   : new
        Usage   : my $obj = Bio::PopGen::IO::prettybase->new();
        Function: Builds a new Bio::PopGen::IO::prettybase object
        Returns : an instance of Bio::PopGen::IO::prettybase
        Args    : -field_delimiter      => a field delimiter character or regexp (default is /\t/ )
                  -header               => boolean if the file will have a header and parser should
                                           skip first line in the file (default is false)
                  -convert_indel_states => convert alleles which are longer than one character
                                           to an 'I' meaning insert state, and alleles which are
                                           '-' to a delete state.
                                           (default is false)

   flag
        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
                  'header', 'field_delimiter', or 'allele_delimiter'
                  on set, new value (a boolean or undef, optional)

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

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

   write_individual
        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)

   write_population
        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