Bio::PopGen::IO - Input individual,marker,allele information use Bio::PopGen::IO; my $io = new Bio::PopGen::IO(-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; } 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.

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/MailList.shtml - About the mailing lists

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: http://bugzilla.bioperl.org/ Email jason-at-bioperl.org Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::PopGen::IO(); 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 SearchIO 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 :