Provided by: libbio-perl-perl_1.6.923-1_all 
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.