Scroll to navigation

Bio::MapIO(3pm) User Contributed Perl Documentation Bio::MapIO(3pm)

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    :
2018-10-27 perl v5.26.2