Bio::Map::Physical(3)

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 = new Bio::MapIO(-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.

Access Methods
These methods let you get and set the member variables

  version
 Title   : version
 Usage   : my $version = $map->version();
 Function: returns the version of the program used to
           generate this map
 Returns : scalar representing the version
 Args    : scalar representing the version

  modification_user
 Title   : modification_user
 Usage   : my $modification_user = $map->modification_user();
 Function: returns the name of the user who last modified this map
 Returns : scalar representing the username
 Args    : [optional] scalar representing the username

  group_type
 Title   : group_type
 Usage   : $map->group_type($grptype); _or_
           my $grptype = $map->group_type();
 Function: get/set the group type of this map
 Returns : scalar representing the group type
 Args    : if provided, the current group type of this map
           will be set to $grptype.

  group_abbr
 Title   : group_abbr
 Usage   : $map->group_abbr($grpabbr); _or_
           my $grpabbr = $map->group_abbr();
 Function: get/set the group abbrev of this map
 Returns : string representing the group abbrev
 Args    : if provided, the current group abbrev of this map
           will be set to $grpabbr.

  core_exists
 Title   : core_exists
 Usage   : my $core_exists = $map->core_exists();
 Function: returns true if the FPC file is accompanied by COR file,
           else false
 Returns : 1 / 0 depending on whether the COR file is present or not.
 Args    : 1 / 0 indicating the presence of COR file

  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.

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/MailList.shtml  - 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.bioperl.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 _