Bio::PopGen::IO(3pm)					User Contributed Perl Documentation				      Bio::PopGen::IO(3pm)

NAME

       Bio::PopGen::IO - Input individual,marker,allele information

SYNOPSIS

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

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

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

DESCRIPTION

       This is a generic interface to reading in population genetic data (of which there really isn't too many standard formats).  This
       implementation makes it easy to provide your own parser for the data.  You need to only implement one function next_individual.	You can
       also implement next_population if your data has explicit information about population memberhsip for the indidviduals.

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

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->new();
	Function: Builds a new Bio::PopGen::IO object
	Returns : an instance of Bio::PopGen::IO
	Args	:

   next_individual
	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

   next_population
	Title	: next_population
	Usage	: my $pop = $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

   write_individual
	Title	: write_individual
	Usage	: $popgenio->write_individual($ind);
	Function: Write an individual out in the implementation 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 implementation format
	Returns : none
	Args	: L<Bio::PopGen::PopulationI> object(s)
	Note	: Many implementation will not implement this

   newFh
	Title	: newFh
	Usage	: $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format')
	Function: does a new() followed by an fh()
	Example : $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format')
		  $sequence = <$fh>;   # read a sequence object
		  print $fh $sequence; # write a sequence object
	Returns : filehandle tied to the Bio::SeqIO::Fh class
	Args	:

       See Bio::SeqIO::Fh

   fh
	Title	: fh
	Usage	: $obj->fh
	Function:
	Example : $fh = $obj->fh;      # make a tied filehandle
		  $sequence = <$fh>;   # read a sequence object
		  print $fh $sequence; # write a sequence object
	Returns : filehandle tied to Bio::SeqIO class
	Args	: none

   _load_format_module
	Title	: _load_format_module
	Usage	: *INTERNAL Bio::PopGen::IO stuff*
	Function: Loads up (like use) a module at run time on demand
	Example :
	Returns :
	Args	:

   _guess_format
	Title	: _guess_format
	Usage	: $obj->_guess_format($filename)
	Function:
	Example :
	Returns : guessed format of filename (lower case)
	Args	:

perl v5.14.2							    2012-03-02						      Bio::PopGen::IO(3pm)