Bio::Map::Clone.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Map::Clone - An central map object representing a clone

SYNOPSIS

    # get the clone object of $clone from the Bio::Map::Clone
    my $cloneobj = $physical->get_cloneobj($clone);
 
    # acquire all the markers that hit this clone
    foreach my $marker ($cloneobj->each_markerid()) {
        print "   +++$marker\n";
    }
 
 

See Bio::Map::Position and Bio::Map::PositionI for more information.

DESCRIPTION

This object handles the notion of a clone. This clone will have a name and a position in a map.

This object is intended to be used by a map parser like fpc.pm.

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::Clone->new
                       (
                        -name    => $clone,
                        -markers => \@markers,
                        -contig  => $contig,
                        -type    => $type,
                        -bands   => $bands,
                        -gel     => $gel,
                        -group   => $group,
                        -remark  => $remark,
                        -fpnumber=> $fp_number,
                        -sequencetype  => $seq_type,
                        -sequencestatus=> $seq_status,
                        -fpcremark => $fpc_remark,
                        -matche    => \@ematch,
                        -matcha    => \@amatch,
                        -matchp    => \@pmatch,
                        -range     => Bio::Range->new(-start => $startrange,
                                                      -end   => $endrange)
                        );
  Function: Initialize a new Bio::Map::Clone object
            Most people will not use this directly but get Clones 
            through L<Bio::MapIO::fpc>
  Returns : L<Bio::Map::Clone> object
  Args    :   -name => marker name string,
              -markers => array ref of markers,
              -contig  => contig name string,
              -type    => type string,
              -bands   => band string,
              -gel     => gel string,
              -group   => group name string,
              -remark  => remark string,
              -fpnumber=> FP number string,
              -sequencetype  => seq type string,
              -sequencestatus=> seq status string,
              -fpcremark => FPC remark,
              -matche    => array ref,
              -matcha    => array ref,
              -matchp    => array ref,
              -range     => L<Bio::Range> object,
 
 

Access Methods

These methods let you get and set the member variables

name

  Title   : name
  Usage   : my $name = $cloneobj->name();
  Function: Get/set the name for this Clone
  Returns : scalar representing the current name of this clone
  Args    : none to get, OR string to set
 
 

type

  Title   : type
  Usage   : my $type = $cloneobj->type();
  Function: Get/set the type for this clone
  Returns : scalar representing the current type of this clone
  Args    : none to get, OR string to set
 
 

range

  Title   : range
  Usage   : my $range = $cloneobj->range();
  Function: Get/set the range of the contig that this clone covers
  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
 
 

match

  Title   : match
  Usage   : @eclone = $cloneobj->match('exact');
            @aclone = $cloneobj->match('approximate');
            @pclone = $cloneobj->match('pseudo');
  Function: get all matching clones
  Returns : list 
  Args    : scalar representing the type of clone to be 
            queried.
 
 

each_match

  Title   : each_match
  Function: Synonym of the match() method.
 
 

set_match

  Title   : set_match
  Usage   : $clone->set_match($type,$values);
  Function: Set the Matches per type
  Returns : None
  Args    : type (one of 'exact' 'approx' 'pseudo')
            array ref of match values
 
 

gel

  Title   : gel
  Usage   : $clonegel = $cloneobj->gel();
  Function: Get/set the gel number for this clone
  Returns : scalar representing the gel number of this clone
  Args    : none to get, OR string to set
 
 

remark

  Title   : remark
  Usage   : $cloneremark = $cloneobj->remark();
  Function: Get/set the remark for this clone
  Returns : scalar representing the current remark of this clone
  Args    : none to get, OR string to set
 
 

fp_number

  Title   : fp_number
  Usage   : $clonefpnumber = $cloneobj->fp_number();
  Function: Get/set the fp number for this clone
  Returns : scalar representing the fp number of this clone
  Args    : none to get, OR string to set
 
 

sequence_type

  Title   : sequence_type
  Usage   : $cloneseqtype = $cloneobj->sequence_type();
  Function: Get/set the sequence type for this clone
  Returns : scalar representing the sequence type of this clone
  Args    : none to get, OR string to set
 
 

sequence_status

  Title   : sequence_status
  Usage   : $cloneseqstatus = $cloneobj->sequence_status();
  Function: Get/set the sequence status for this clone
  Returns : scalar representing the sequence status of this clone
  Args    : none to get, OR string to set
 
 

fpc_remark

  Title   : fpc_remark
  Usage   : $clonefpcremark = $cloneobj->fpc_remark();
  Function: Get/set the fpc remark for this clone
  Returns : scalar representing the fpc remark of this clone
  Args    : none to get, OR string to set
 
 

bands

  Title   : bands
  Usage   : @clonebands = $cloneobj->bands();
  Function: Get/set the bands for this clone
  Returns : liat representing the band of this clone, if 
            readcor = 1 while creating the MapIO object and the
            .cor exists
  Args    : none to get, OR string to set
 
 

group

  Title   : group
  Usage   : $cloneobj->group($chrno);
  Function: Get/set the group number for this clone.
            This is a generic term, used for Linkage-Groups as well as for
            Chromosomes.
  Returns : scalar representing the group number of this clone
  Args    : none to get, OR string to set
 
 

contigid

  Title   : contigid
  Usage   : my $ctg = $cloneobj->contigid();
  Function: Get/set the contig this clone belongs to
  Returns : scalar representing the contig
  Args    : none to get, OR string to set
 
 

each_markerid

  Title   : each_markerid
  Usage   : @markers = $cloneobj->each_markerid();
  Function: retrieves all the elements 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_markers

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