Bio::Map
Clone
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Summary
Bio::Map::Clone - An central map object representing a clone
Package variables
No package variables defined.
Included modules
Inherit
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.
Methods
Methods description
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 Bio::MapIO::fpc
Returns : 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 => Bio::Range object, |
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 |
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 |
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 |
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. |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 *** |
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 *** |
Methods code
sub new
{ my ($class,@args) = @_;
my $self= $class->SUPER::new(@args);
my ($name,$markers,$contig,$type,$bands,$gel,$group,
$remark,$fpnumber,$seqtype,$seqstatus,$fpcremark,
$matche,$matcha,$matchp,
$range) = $self->_rearrange([qw(NAME MARKERS CONTIG TYPE
BANDS GEL GROUP REMARK FPNUMBER
SEQUENCETYPE SEQUENCESTATUS
FPCREMARK MATCHE MATCHA MATCHP
RANGE)],@args);
$self->name($name) if defined $name;
$self->markers($markers) if defined $markers;
$self->contigid($contig) if defined $contig;
$self->type($type) if defined $type;
$self->bands($bands) if defined $bands;
$self->gel($gel) if defined $gel;
$self->group($group) if defined $group;
$self->remark($remark) if defined $remark;
$self->fp_number($fpnumber) if defined $fpnumber;
$self->sequence_type($seqtype) if defined $seqtype;
$self->sequence_status($seqstatus) if defined $seqstatus;
$self->fpc_remark($fpcremark) if defined $fpcremark;
$self->range($range) if defined $range;
$self->set_match('approx', $matcha) if defined $matcha;
$self->set_match('pseudo', $matchp) if defined $matchp;
$self->set_match('exact', $matche) if defined $matche;
return $self;} | sub name
{ my ($self) = shift;
return $self->{'_name'} = shift if @_;
return $self->{'_name'};} | sub type
{ my ($self) = shift;
return $self->{'_type'} = shift if @_;
return $self->{'_type'};} | sub range
{ my ($self) = shift;
return $self->{'_range'} = shift if @_;
return $self->{'_range'};} | sub match
{ my ($self,$type) = @_;
$type = "_match" . lc(substr($type, 0, 1));
return @{$self->{$type} || []};} | sub set_match
{ my ($self,$type,$val) = @_;
$type = "_match" . lc(substr($type, 0, 1));
$self->{$type} = $val;} | sub gel
{ my ($self) = shift;
return $self->{'_gel'} = shift if @_;
return $self->{'_gel'};} | sub remark
{ my ($self) = shift;
return $self->{'_remark'} = shift if @_;
return $self->{'_remark'};} | sub fp_number
{ my ($self) = shift;
return $self->{'_fpnumber'} = shift if @_;
return $self->{'_fpnumber'};} | sub sequence_type
{ my ($self) = shift;
return $self->{'_sequencetype'} = shift if @_;
return $self->{'_sequencetype'};} | sub sequence_status
{ my ($self) = shift;
return $self->{'_sequencestatus'} = shift if @_;
return $self->{'_sequencestatus'};} | sub fpc_remark
{ my ($self) = shift;
return $self->{'_fpcremark'} = shift if @_;
return $self->{'_fpcremark'};} | sub bands
{ my ($self) = shift;
return $self->{'_bands'} = shift if @_;
return $self->{'_bands'};} | sub group
{ my ($self) = shift;
return $self->{'_group'} = shift if @_;
return $self->{'_group'};} | sub contigid
{ my ($self) = shift;
$self->{'_contig'} = shift if @_;
return $self->{'_contig'} || 0;} | sub each_markerid
{ my ($self,$value) = @_;
return @{$self->{"_markers"}};} | sub set_markers
{ my ($self,$markers) = @_;
if( defined $markers && ref($markers) =~ /ARRAY/ ) {
$self->{'_markers'} = $markers;
}
}
1;} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
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bioperl-l@bioperl.org - General discussion
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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.
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://redmine.open-bio.org/projects/bioperl/
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.eduThe rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
These methods let you get and set the member variables
Title : each_match
Function: Synonym of the match() method.