/ 
BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::MapIO::fpc

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 _