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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:

   http://bugzilla.open-bio.org/
 
 

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    :