Bio::Map::Physical.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

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:
   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 _

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]
 
 
  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
 
 
  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
 
 
  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.