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Man Pages


Manual Reference Pages  -  BIO::MAPIO::FPC (3)

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NAME

Bio::MapIO::fpc - A FPC Map reader

CONTENTS

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 : doesnt 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 _
Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::MAPIO::FPC (3) 2016-04-05

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