The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
BioPerl-1.007000_005
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Map::Clone

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:

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

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 ***