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Bio::PopGen::IO::hapmap.3pm

NAME

Bio::PopGen::IO::hapmap - A parser for HapMap output data

SYNOPSIS

   # Do not use directly, use through the Bio::PopGen::IO driver
 
   use Bio::PopGen::IO;
   my $io = Bio::PopGen::IO->new(-format => 'hapmap',
                                -file   => 'data.hapmap');
 
   # 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 hapmap data.

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,
            -starting_column => 11
 
 

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 : A Bio::PopGen::IndividualI object
  Args    : none
 
 

See Bio::PopGen::IndividualI

next_population

  Title   : next_population
  Usage   : my $ind = $popgenio->next_population;
  Function: Retrieve the next population from a dataset
  Returns : Bio::PopGen::PopulationI object
  Args    : none
  Note    : Many implementation will not implement this
 
 

See Bio::PopGen::PopulationI

write_individual

  Title   : write_individual
  Usage   : $popgenio->write_individual($ind);
  Function: Write an individual out in the file format
            NOT SUPPORTED  BY hapmap format
  Returns : none
  Args    : Bio::PopGen::PopulationI object(s)
 
 

See Bio::PopGen::PopulationI

write_population

  Title   : write_population
  Usage   : $popgenio->write_population($pop);
  Function: Write a population out in the file format
            NOT SUPPORTED  BY hapmap format
  Returns : none
  Args    : Bio::PopGen::PopulationI object(s)
  Note    : Many implementation will not implement this
 
 

See Bio::PopGen::PopulationI

starting_column

  Title   : starting_column
  Usage   : $obj->starting_column($newval)
  Function: Column where data starts
  Example : 
  Returns : value of starting_column (a scalar)
  Args    : on set, new value (a scalar or undef, optional)