diff variant_effect_predictor/Bio/MapIO/mapmaker.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/MapIO/mapmaker.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,150 @@
+# $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 <[e-mail]>
+#
+# 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.
+
+  [e-mail]              - 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:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Jason Stajich
+
+Email [e-mail]
+
+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;