NAME

Bio::MapIO - A Map Factory object

SYNOPSIS

    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 is the Factory object for reading Maps from a data stream or file.

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 the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason@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::MapIO->new();
Function: Builds a new Bio::MapIO object 
Returns : Bio::MapIO
Args    :

format

Title   : format
Usage   : $format = $stream->format()
Function: Get the map format
Returns : map format
Args    : none

Bio::Factory::MapFactoryI methods

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

write_map

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

attach_EventHandler

Title   : attach_EventHandler
Usage   : $parser->attatch_EventHandler($handler)
Function: Adds an event handler to listen for events
Returns : none
Args    : L<Bio::Event::EventHandlerI>

_eventHandler

Title   : _eventHandler
Usage   : private
Function: Get the EventHandler
Returns : L<Bio::Event::EventHandlerI>
Args    : none

_load_format_module

Title   : _load_format_module
Usage   : *INTERNAL MapIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args    :

_guess_format

Title   : _guess_format
Usage   : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args    :

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq