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Man Pages


Manual Reference Pages  -  BIO::MAP::CLONE (3)

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NAME

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

CONTENTS

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 ***



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