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Bio::PopGen::IO::phase.3pm

NAME

Bio::PopGen::IO::phase - A parser for Phase format data

SYNOPSIS

# Do not use directly, use through the Bio::PopGen::IO driver

   use Bio::PopGen::IO;
   my $io = Bio::PopGen::IO->new(-format => 'phase',
                                -file   => 'data.phase');
 
   # Some IO might support reading in a population at a time
 
   my @population;
   while( my $ind = $io->next_individual ) {
       push @population, $ind;
   }
 
 

DESCRIPTION

A driver module for Bio::PopGen::IO for parsing phase data.

PHASE is defined in http://www.stat.washington.edu/stephens/instruct2.1.pdf

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 - Rich Dobson

Email r.j.dobson-at-qmul.ac.uk

CONTRIBUTORS

Jason Stajich, 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::hapmap->new();
  Function: Builds a new Bio::PopGen::IO::hapmap object 
  Returns : an instance of Bio::PopGen::IO::hapmap
  Args    : [optional, these are the current defaults] 
            -field_delimiter => ','
            -allele_delimiter=> '\s+'
            -no_header       => 0,
 
 

flag

  Title   : flag
  Usage   : $obj->flag($flagname,$newval)
  Function: Get/Set the flag value
  Returns : value of a flag (a boolean)
  Args    : A flag name, currently we expect 
            'no_header', 'field_delimiter', or 'allele_delimiter' 
            on set, new value (a boolean or undef, optional)
 
 

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 $ind = $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 file 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 file format
  Returns : none
  Args    : L<Bio::PopGen::PopulationI> object(s)
  Note    : Many implementation will not implement this