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

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,

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 ***