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Summary

Bio::MapIO::mapmaker - A Mapmaker Map reader

Package variables

Included modules

Inherit

Bio::MapIO

Synopsis

# do not use this object directly it is accessed through the Bio::MapIO system

    use Bio::MapIO;
    my $mapio = Bio::MapIO->new(-format => "mapmaker",
			                      -file   => "mapfile.map");
    while ( my $map = $mapio->next_map ) {  # get each map
	    foreach my $marker ( $map->each_element ) {
	       # loop through the markers associated with the map
	    }
    }

Description

This object contains code for parsing and processing Mapmaker output
and creating Bio::Map::MapI objects from it.

Methods

Methods description

 Title   : next_map
 Usage   : my $map = $factory->next_map;
 Function: Get one or more map objects from the Mapmaker input
 Returns : Bio::Map::MapI
 Args    : none

 Title   : write_map
 Usage   : $factory->write_map($map);
 Function: Write a map out through the factory
 Returns : none
 Args    : Bio::Map::MapI

Methods code

sub next_map {

   my ($self) = @_;
   my $map = Bio::Map::SimpleMap->new(-name  => '',
												  -units => 'cM',
												  -type  => 'Genetic');

	# Mapmaker input can be free-form, like the result of a copy-paste
	# from a terminal, with no particular format before or after the 
	# map data. The $in_map variable is a flag that's set to 1 when 
	# we're reading map data lines and set back to 0 when we're finished.
   my ($in_map,$runningDistance);

   while ( defined ($_ = $self->_readline()) ) {
		if ( /^\s+Markers\s+Distance/ ) {
			$in_map = 1;
			next;
		} 
		next unless $in_map;
 
		s/ +/\t/;
		my ($number,$name,$distance) = split;
		$runningDistance += $distance unless ($distance =~ /-+/);
		$runningDistance = '0.0' if ($runningDistance == 0 || $distance =~ /-+/);

		my $pos = Bio::Map::LinkagePosition->new(-order => $number,
															 -map   => $map,
															 -value => $runningDistance );
		my $marker = Bio::Map::Marker->new(-name     => $name,
													 -position => $pos );
		
		if ($distance =~ /-+/) { # last marker
			$in_map = 0;
			return $map;
		}  
	}

}

sub write_map {

   my ($self,@args) = @_;
   $self->throw_not_implemented();
}

1;

}

General documentation

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

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.

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://redmine.open-bio.org/projects/bioperl/

Email jason@bioperl.org

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _