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    :

format

Title   : format
Usage   : $format = $stream->format()
Function: Get the PopGen format
Returns : PopGen format
Args    : none

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    :

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq