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 _