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)