Bio::Map::FPCMarker.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Map::FPCMarker - An central map object representing a marker

SYNOPSIS

    # get the marker object of $marker from the Bio::Map::FPCMarker
    my $markerobj = $physical->get_markerobj($marker);
 
    # acquire all the clones that hit this marker
    foreach my $clone ($markerobj->each_cloneid()) {
        print "   +++$clone\n";
    }
 
    # find the position of this marker in $contig
    print "Position in contig $contig"," = ",$markerobj->position($contig),
          "\n";
 
    # find the group of the marker
    print "Group : ",$markerobj->group();
 
 

See Bio::Map::Position and Bio::Map::PositionI for more information.

DESCRIPTION

This object handles the notion of a marker. This object is intended to be used by a map parser like fpc.pm.

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

AUTHOR - Gaurav Gupta

Email gaurav@genome.arizona.edu

CONTRIBUTORS

Sendu Bala bix@sendu.me.uk

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 _

new

  Title   : new
  Usage   : my $clone = Bio::Map::FPCMarker->new
                       (
                        -name    => $marker,
                        -type    => $type,
                        -global  => $global,
                        -frame   => $frame,
                        -group   => $group,
                        -subgroup=> $subgroup,
                        -anchor  => $anchor,
                        -clones  => \%clones,
                        -contigs => \%contigs,
                        -position => \%markerpos,
                -remark => $remark
                        );
 
  Function: Initialize a new Bio::Map::FPCMarker object
            Most people will not use this directly but get Markers
            through L<Bio::MapIO::fpc>
  Returns : L<Bio::Map::FPCMarker> object
  Args    : -name     => marker name string,
                -type     => type string,
                -global   => global position for marker,
                -frame    => boolean if marker is framework or placement,
                -group    => group number for marker,
                -subgroup => subgroup number of marker,
                -anchor   => boolean if marker is anchored,
                -clones   => all the clone elements in map (hashref),
                -contigs  => all the contig elements (hasref),
                -position => mapping of marker names to map position (hasref),
            -remark   => remarks, separated by newlines
 
 

Access Methods

These methods let you get and set the member variables

name

  Title   : name
  Usage   : my $name = $markerobj->name();
  Function: Get/set the name for this marker
  Returns : scalar representing the current name of this marker
  Args    : none to get, OR string to set
 
 

type

  Title   : type
  Usage   : my $type = $markerobj->type();
  Function: Get/set the type for this marker
  Returns : scalar representing the current type of this marker
  Args    : none to get, OR string to set
 
 

global

  Title   : global
  Usage   : my $type = $markerobj->global();
  Function: Get/set the global position for this marker
  Returns : scalar representing the current global position of this marker
  Args    : none to get, OR string to set
 
 

anchor

  Title   : anchor
  Usage   : my $anchor = $markerobj->anchor();
  Function: indicate if the Marker is anchored or not (True | False)
  Returns : scalar representing the anchor (1 | 0) for this marker
  Args    : none to get, OR 1|0 to set
 
 

framework

  Title   : framework
  Usage   : $frame = $markerobj->framework();
  Function: indicate if the Marker is framework or placement (1 | 0)
  Returns : scalar representing if the marker is framework
            (1 if framework, 0 if placement)
  Args    : none to get, OR 1|0 to set
 
 

group

  Title   : group
  Usage   : $grpno = $markerobj->group();
  Function: Get/set the group number for this marker. This is a generic term,
            used for Linkage-Groups as well as for Chromosomes.
  Returns : scalar representing the group number of this marker
  Args    : none to get, OR string to set
 
 

subgroup

  Title   : subgroup
  Usage   : $subgroup = $marker->subgroup();     
  Function: Get/set the subgroup for this marker. This is a generic term:
            subgroup here could represent subgroup of a Chromosome or of a
            Linkage Group. The user must take care of which subgroup he/she is
            querying for.        
  Returns : scalar representing the subgroup of this marker
  Args    : none to get, OR string to set
 
 

position

  Title   : position
  Usage   : $markerpos = $markerobj->position($ctg);
  Function: get the position of the marker in the contig
  Returns : scalar representing the position of the markernumber of
            the contig
  Args    : $ctg is necessary to look for the position of the marker
            in that contig.
 
  *** This has nothing to do with an actual Bio::Map::PositionI object ***
 
 

remark

  Title   : remark
  Usage   : $markerremark = $markerobj->remark();
  Function: get the remarks for this marker
  Returns : scalar of newline-separated markers
  Args    : none
 
 

each_cloneid

  Title   : each_cloneid
  Usage   : my @clones  = $map->each_cloneid();
  Function: retrieves all the clone ids in a map unordered
  Returns : list of strings (ids)
  Args    : none
 
  *** This only supplies the ids set with the set_clones method ***
  *** It has nothing to do with actual Bio::Map::MappableI objects ***
 
 

each_contigid

  Title   : each_contigid
  Usage   : my @contigs = $map->each_contigid();
  Function: retrieves all the contig ids in a map unordered
  Returns : list of strings (ids)
  Args    : none
 
  *** This only supplies the ids set with the set_contigs method ***
  *** It has nothing to do with actual Bio::Map::MapI objects ***
 
 

set_clones

  Title   : set_clones
  Usage   : $marker->set_clones(\%clones)
  Function: Set the clone ids hashref
  Returns : None
  Args    : Hashref of clone ids
 
  *** This only sets a hash of ids ***
  *** It has nothing to do with actual Bio::Map::MappableI objects ***
 
 

set_contigs

  Title   : set_contigs
  Usage   : $marker->set_contigs(\%contigs)
  Function: Set the contig ids hashref
  Returns : None
  Args    : Hashref of contig ids
 
  *** This only sets a hash of ids ***
  *** It has nothing to do with actual Bio::Map::MapI objects ***
 
 

set_positions

  Title   : set_positions
  Usage   : $marker->set_positions(\%markerpos)
  Function: Set the positions hashref
  Returns : None
  Args    : Hashref of marker positions
 
  *** This only sets a hash of numbers ***
  *** It has nothing to do with actual Bio::Map::PositionI objects ***