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

NAME

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

SYNOPSIS

       # 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.
	   }

DESCRIPTION

       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 overhead.

Initializer
   _initialize
	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

   next_map
	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

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

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Gaurav Gupta
       Email gaurav@genome.arizona.edu

PROJECT LEADERS

       Jamie Hatfield		 jamie@genome.arizona.edu

       Dr. Cari Soderlund	 cari@genome.arizona.edu

PROJECT DESCRIPTION

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

       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:
	 http://www.genome.arizona.edu

APPENDIX

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

perl v5.14.2							    2012-03-02						      Bio::MapIO::fpc(3pm)