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

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

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 v5.24.1			  2017-07-08		    Bio::MapIO::fpc(3)

NAME | SYNOPSIS | DESCRIPTION | Initializer | Access Methods | FEEDBACK | AUTHOR - Gaurav Gupta | PROJECT LEADERS | PROJECT DESCRIPTION | APPENDIX

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