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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Gaurav Gupta

Email [email protected]

CONTRIBUTORS

Sendu Bala [email protected]

PROJECT LEADERS

Jamie Hatfield [email protected] Dr. Cari Soderlund [email protected]

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 ***