Christopher Fields > BioPerl > Bio::MapIO::mapmaker

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Module Version: 1.006924   Source  

NAME ^

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

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.

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 via 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 _

next_map

 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

See Bio::Map::MapI

write_map

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