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Manual Reference Pages  -  BIO::POPGEN::IO::PHASE (3)

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NAME

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

CONTENTS

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:



  https://github.com/bioperl/bioperl-live/issues



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



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perl v5.20.3 BIO::POPGEN::IO::PHASE (3) 2016-04-05

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