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Bio::Map::Contig.3pm

NAME

Bio::Map::Contig - A MapI implementation handling the contigs of a Physical Map (such as FPC)

SYNOPSIS

     # get the contig object of $contig from the Bio::Map::Physical
     my $ctgobj = $physical->get_contigobj($contig);
 
     # acquire all the markers that lie in this contig
     foreach my $marker ($ctgobj->each_markerid()) {
         print "   +++$marker\n";
     }
 
     # find the group of this contig
     print "Group: ",$ctgobj->group(),"\n";
 
     # find the range of this contig
     print "RANGE: start:",$ctgobj->range()->start(),"\tend: ",
            $ctgobj->range()->end(),"\n";
 
     # find the position of this contig in $group (chromosome)
     print "Position in Group $group"," = ",$ctgobj->position($group),"\n";
 
 

DESCRIPTION

This is an implementation of Bio::Map::MapI. It handles the essential storage of name, species, type, and units as well as in memory representation of the elements of a map.

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

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::Contig->new
                       (
                        -name    => $name,
                        -chr_remark   => $cremark,
                        -user_remark  => $uremark,
                        -trace_remark => $tremark,
                        -group   => $group,
                        -subgroup=> $subgroup,
                        -anchor  => $anchor,
                        -markers => \%markers,
                        -clones  => \%clones,
                        -position => $pos
                        -range    => Bio::Range->new(-start =>$s,-end=>$e),
                        );
 
  Function: Initialize a new Bio::Map::Contig object
            Most people will not use this directly but get Markers
            through L<Bio::MapIO::fpc>
  Returns : L<Bio::Map::Contig> object
  Args    : ( -name    => name string,
              -chr_remark   => chr remark string,
              -user_remark  => userremark string,
              -trace_remark => tremark string,
              -group   => group string,
              -subgroup=> subgroup string,
              -anchor  => boolean if this is anchored or not,
              -markers => hashref of contained markers,
              -clones  => hashref of contained clones,
              -position => position
              -range    => L<Bio::Range>
 
 

Modifier methods

All methods present in Bio::Map::SimpleMap are implemented by this class. Most of the methods are inherited from SimpleMap. The following methods have been modified to reflect the needs of physical maps.

chr_remark

  Title   : chr_remark
  Usage   : my $chrremark = $contigobj->chr_remark();
  Function: Get/set the group remark for this contig
  Returns : scalar representing the current group_remark of this contig
  Args    : none to get, OR string to set
 
 

user_remark

  Title   : user_remark
  Usage   : my $userremark = $contigobj->user_remark();
  Function: Get/set the user remark for this contig
  Returns : scalar representing the current user_remark of this contig
  Args    : none to get, OR string to set
 
 

trace_remark

  Title   : trace_remark
  Usage   : my $traceremark = $contigobj->trace_remark();
  Function: Get/set the trace remark for this contig
  Returns : scalar representing the current trace_remark of this contig
  Args    : none to get, OR string to set
 
 

range

  Title   : range
  Usage   : my $range = $contigobj->range();
  Function: Get/set the range for this Contig
  Returns : Bio::Range representing the current range of this contig,
            start and end of the contig can be thus found using:
            my $start = $contigobj->range()->start();
            my $end   = $contigobj->range()->end();
  Args    : none to get, OR Bio::Range to set
 
 

position

  Title   : position
  Usage   : $ctgpos = $contigobj->position();
  Function: Get/set the position of the contig in the group
  Returns : scalar representing the position of the contig in the group
  Args    : none to get, OR string to set
 
 

anchor

  Title   : anchor
  Usage   : $ctganchor = $contig->anchor();
  Function: Get/set the anchor value for this Contig (True | False)
  Returns : scalar representing the anchor (1 | 0) for this contig
  Args    : none to get, OR string to set
 
 

group

  Title   : group
  Usage   : $groupno = $contigobj->group();
  Function: Get/set the group number for this contig.
            This is a generic term, used for Linkage-Groups as well as for
            Chromosomes. 
  Returns : scalar representing the group number of this contig
  Args    : none
 
 

subgroup

  Title   : subgroup
  Usage   : $subgroup = $contig->subgroup();     
  Function: Get/set the subgroup for this contig. 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 : A scalar representing the subgroup of this contig
  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_markerid

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

set_clones

  Title   : set_clones
  Usage   : $marker->set_clones(\%clones)
  Function: Set the clones 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_markers

  Title   : markers
  Usage   : $obj->set_markers($newval)
  Function: Set list of Markers (hashref)
  Returns : None
  Args    : Hashref of marker ids
 
  *** This only sets a hash of ids ***
  *** It has nothing to do with actual Bio::Map::MarkerI objects ***