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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 = new Bio::MapIO(-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
 
 

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:

   http://bugzilla.open-bio.org/
 
 

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 _