Scroll to navigation

Bio::PopGen::IO::hapmap(3pm) User Contributed Perl Documentation 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:

  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,
           -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)
2018-10-27 perl v5.26.2