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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 :
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 $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
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)
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
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
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
Title : _load_format_module Usage : *INTERNAL SearchIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :
Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args :
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.