Provided by: libbio-perl-perl_1.7.2-3_all bug


       Bio::MapIO::fpc - A FPC Map reader


       # do not use this object directly it is accessed through the Bio::MapIO system

           use Bio::MapIO;

            -format  : specifies the format of the file format is "fpc",
            -file    : specifies the name of the .fpc file
            -readcor : boolean argument, indicating if .cor is to be read
                        or not. It looks for the .cor file in the same path
                        as .fpc file.
                        0 : doesn't read .cor file
                        1 : reads the .cor file
                        [default 0]
            -verbose : indicates the process of loading of fpc file
           my $mapio = Bio::MapIO->new(-format  => "fpc",
                                      -file    => "rice.fpc",
                                      -readcor => 0,
                                      -verbose => 0);

           my $map = $mapio->next_map();

           foreach my $marker ( $map->each_markerid() ) {
                # loop through the markers associated with the map
                # likewise for contigs, clones, etc.


       This object contains code for parsing and processing FPC files and creating
       Bio::Map::Physical object from it.

       For faster access and better optimization, the data is stored internally in hashes. The
       corresponding objects are created on request.

       We handle reading of the FPC ourselves, since MapIO module of Bioperl adds too much


        Title   : _initialize
        Usage   : called implicitly
        Function: calls the SUPER::_initialize
        Returns : nothing
        Args    : species, readcor

Access Methods

       These methods let you get and set the member variables

        Title   : next_map
        Usage   : my $fpcmap = $mapio->next_map();
        Function: gets the fpcmap from MapIO
        Returns : object of type L<Bio::Map::MapI>
        Args    : none

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


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AUTHOR - Gaurav Gupta



       Jamie Hatfield  

       Dr. Cari Soderlund


       The project was done in Arizona Genomics Computational Laboratory (AGCoL) at University of

       This work was funded by USDA-IFAFS grant #11180 titled "Web Resources for the Computation
       and Display of Physical Mapping Data".

       For more information on this project, please refer:


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _