Raw content of Bio::MapIO::mapmaker
<![CDATA[# $Id: mapmaker.pm,v 1.5 2002/10/22 07:45:16 lapp Exp $
#
# BioPerl module for Bio::MapIO::mapmaker
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::MapIO::mapmaker - A Mapmaker Map reader
=head1 SYNOPSIS
# do not use this object directly it is accessed through the Bio::MapIO system
use Bio::MapIO;
my $mapio = new Bio::MapIO(-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
}
}
=head1 DESCRIPTION
This object contains code for parsing and processing Mapmaker output
and creating L<Bio::Map::MapI> objects from it.
=head1 FEEDBACK
=head2 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/MailList.shtml - About the mailing lists
=head2 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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::MapIO::mapmaker;
use vars qw(@ISA);
use strict;
use Bio::MapIO;
use Bio::Map::SimpleMap;
use Bio::Map::LinkagePosition;
use Bio::Map::Marker;
@ISA = qw(Bio::MapIO );
=head2 next_map
Title : next_tree
Usage : my $map = $factory->next_map;
Function: Get a map from the factory
Returns : L<Bio::Map::MapI>
Args : none
=cut
sub next_map{
my ($self) = @_;
my ($ready,$map) = (0,new Bio::Map::SimpleMap('-name' => '',
'-units' => 'cM',
'-type' => 'Genetic'));
my @markers;
my $runningDistance = 0;
while( defined($_ = $self->_readline()) ) {
if ( $ready || /^\s+Markers\s+Distance/ ) {
unless ( $ready ) { $ready = 1; next }
} else { next }
last if ( /-{5,}/); # map terminator is -------
s/ +/\t/;
my ($number,$name,$distance) = split;
$runningDistance += $distance;
$runningDistance = '0.0' if $runningDistance == 0;
# print "$_|$number-$name-$distance---------";
my $pos = new Bio::Map::LinkagePosition (-order => $number,
-map => $map,
-value => $runningDistance
);
my $marker = new Bio::Map::Marker(-name=> $name,
-position => $pos,
);
$marker->position($pos);
# use Data::Dumper; print Dumper($marker); exit;
# print $marker->position->value, "\n";
# use Data::Dumper; print Dumper($pos);
# $map->add_element(new Bio::Map::Marker('-name'=> $name,
# '-position' => $pos,
# ));
}
# return undef if( ! $ready );
return $map;
}
=head2 write_map
Title : write_tree
Usage : $factory->write_map($map);
Function: Write a map out through the factory
Returns : none
Args : Bio::Map::MapI
=cut
sub write_map{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
1;
]]>