Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Map::Physical - A class for handling a Physical Map (such as FPC)

SYNOPSIS

           use Bio::MapIO;

           # accquire a Bio::Map::Physical using Bio::MapIO::fpc
           my $mapio = Bio::MapIO->new(-format => "fpc",-file => "rice.fpc",
                                      -readcor => 0);

           my $physical = $mapio->next_map();

           # get all the markers ids
           foreach my $marker ( $physical->each_markerid() ) {
             print "Marker $marker\n";

             # acquire the marker object using Bio::Map::FPCMarker
             my $markerobj = $physical->get_markerobj($marker);

             # get all the clones hit by this marker
             foreach my $clone ($markerobj->each_cloneid() ) {
                 print " +++$clone\n";
             }
         }

DESCRIPTION

       This class is basically a continer class for a collection of Contig maps and other
       physical map information.

       Bio::Map::Physical has been tailored to work for FPC physical maps, but could probably be
       used for others as well (with the appropriate MapIO module).

       This class also has some methods with specific functionalities:

         print_gffstyle()     : Generates GFF; either Contigwise[Default] or
                                Groupwise

         print_contiglist()   : Prints the list of Contigs, markers that hit the
                                contig, the global position and whether the marker
                                is a placement (<P>) or a Framework (<F>) marker.

         print_markerlist()   : Prints the markers list; contig and corresponding
                                number of clones.

         matching_bands()     : Given two clones [and tolerence], this method
                                calculates how many matching bands do they have.

         coincidence_score()  : Given two clones [,tolerence and gellen], this
                                method calculates the Sulston Coincidence score.

       For faster access and better optimization, the data is stored internally in hashes. The
       corresponding objects are created on request.

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

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 _

Access Methods

       These methods let you get and set the member variables

   version
        Title   : version
        Usage   : my $version = $map->version();
        Function: Get/set the version of the program used to
                  generate this map
        Returns : scalar representing the version
        Args    : none to get, OR string to set

   modification_user
        Title   : modification_user
        Usage   : my $modification_user = $map->modification_user();
        Function: Get/set the name of the user who last modified this map
        Returns : scalar representing the username
        Args    : none to get, OR string to set

   group_type
        Title   : group_type
        Usage   : $map->group_type($grptype);
                      my $grptype = $map->group_type();
        Function: Get/set the group type of this map
        Returns : scalar representing the group type
        Args    : none to get, OR string to set

   group_abbr
        Title   : group_abbr
        Usage   : $map->group_abbr($grpabbr);
                      my $grpabbr = $map->group_abbr();
        Function: get/set the group abbrev of this map
        Returns : string representing the group abbrev
        Args    : none to get, OR string to set

   core_exists
        Title   : core_exists
        Usage   : my $core_exists = $map->core_exists();
        Function: Get/set if the FPC file is accompanied by COR file
        Returns : boolean
        Args    : none to get, OR 1|0 to set

   each_cloneid
        Title   : each_cloneid
        Usage   : my @clones = $map->each_cloneid();
        Function: returns an array of clone names
        Returns : list of clone names
        Args    : none

   get_cloneobj
        Title   : get_cloneobj
        Usage   : my $cloneobj = $map->get_cloneobj('CLONEA');
        Function: returns an object of the clone given in the argument
        Returns : object of the clone
        Args    : scalar representing the clone name

   each_markerid
        Title   : each_markerid
        Usage   : my @markers = $map->each_markerid();
        Function: returns list of marker names
        Returns : list of marker names
        Args    : none

   get_markerobj
        Title   : get_markerobj
        Usage   : my $markerobj = $map->get_markerobj('MARKERA');
        Function: returns an object of the marker given in the argument
        Returns : object of the marker
        Args    : scalar representing the marker name

   each_contigid
        Title   : each_contigid
        Usage   : my @contigs = $map->each_contigid();
        Function: returns a list of contigs (numbers)
        Returns : list of contigs
        Args    : none

   get_contigobj
        Title   : get_contigobj
        Usage   : my $contigobj = $map->get_contigobj('CONTIG1');
        Function: returns an object of the contig given in the argument
        Returns : object of the contig
        Args    : scalar representing the contig number

   matching_bands
        Title   : matching_bands
        Usage   : $self->matching_bands('cloneA','cloneB',[$tol]);
        Function: given two clones [and tolerence], this method calculates how many
                  matching bands do they have.
                  (this method is ported directly from FPC)
        Returns : scalar representing the number of matching bands
        Args    : names of the clones ('cloneA', 'cloneB') [Default tolerence=7]

   coincidence_score
        Title   : coincidence_score
        Usage   : $self->coincidence_score('cloneA','cloneB'[,$tol,$gellen]);
        Function: given two clones [,tolerence and gellen], this method calculates
                  the Sulston Coincidence score.
                  (this method is ported directly from FPC)
        Returns : scalar representing the Sulston coincidence score.
        Args    : names of the clones ('cloneA', 'cloneB')
                  [Default tol=7 gellen=3300.0]

   print_contiglist
        Title   : print_contiglist
        Usage   : $map->print_contiglist([showall]); #[Default 0]
        Function: prints the list of contigs, markers that hit the contig, the
                  global position and whether the marker is a placement (P) or
                  a Framework (F) marker.
        Returns : none
        Args    : [showall] [Default 0], 1 includes all the discrepant markers

   print_markerlist
        Title    : print_markerlist
        Usage    : $map->print_markerlist();
        Function : prints the marker list; contig and corresponding number of
                   clones for each marker.
        Returns  : none
        Args     : none

   print_gffstyle
        Title    : print_gffstyle
        Usage    : $map->print_gffstyle([style]);
        Function : prints GFF; either Contigwise (default) or Groupwise
        Returns  : none
        Args     : [style] default = 0 contigwise, else
                                     1 groupwise (chromosome-wise).

   _calc_markerposition
        Title   : _calc_markerposition
        Usage   : $map->_calc_markerposition();
        Function: Calculates the position of the marker in the contig
        Returns : none
        Args    : none

   _calc_contigposition
        Title   : _calc_contigposition
        Usage   : $map->_calc_contigposition();
        Function: calculates the position of the contig in the group
        Returns : none
        Args    : none

   _calc_contiggroup
        Title   : _calc_contiggroup
        Usage   : $map->_calc_contiggroup();
        Function: calculates the group of the contig
        Returns : none
        Args    : none

   _set<Type>Ref
        Title   : _set<Type>Ref
        Usage   : These are used for initializing the reference of the hash in
                  Bio::MapIO (fpc.pm) to the corresponding hash in Bio::Map
                  (physical.pm). Should be used only from Bio::MapIO System.
                      $map->setCloneRef(\%_clones);
                      $map->setMarkerRef(\%_markers);
                      $map->setContigRef(\%_contigs);
        Function: sets the hash references to the corresponding hashes
        Returns : none
        Args    : reference of the hash.