Bio::Coordinate Collection
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Coordinate::Collection - Noncontinuous match between two coordinate sets
Package variables
No package variables defined.
Included modules
Bio::Coordinate::Result
Bio::Coordinate::Result::Gap
Inherit
Bio::Coordinate::MapperI Bio::Root::Root
Synopsis
  # create Bio::Coordinate::Pairs or other Bio::Coordinate::MapperIs somehow
$pair1; $pair2;
# add them into a Collection $collection = Bio::Coordinate::Collection->new; $collection->add_mapper($pair1); $collection->add_mapper($pair2); # create a position and map it $pos = Bio::Location::Simple->new (-start => 5, -end => 9 ); $res = $collection->map($pos); $res->match->start == 1; $res->match->end == 5; # if mapping is many to one (*>1) or many-to-many (*>*) # you have to give seq_id not get unrelevant entries $pos = Bio::Location::Simple->new (-start => 5, -end => 9 -seq_id=>'clone1');
Description
Generic, context neutral mapper to provide coordinate transforms
between two disjoint coordinate systems. It brings into Bioperl the
functionality from Ewan Birney's Bio::EnsEMBL::Mapper ported into
current bioperl.
This class is aimed for representing mapping between whole chromosomes
and contigs, or between contigs and clones, or between sequencing
reads and assembly. The submaps are automatically sorted, so they can
be added in any order.
To map coordinates to the other direction, you have to swap() the
collection. Keeping track of the direction and ID restrictions
are left to the calling code.
Methods
new
No description
Code
add_mapperDescriptionCode
mappersDescriptionCode
each_mapperDescriptionCode
mapper_countDescriptionCode
swapDescriptionCode
testDescriptionCode
mapDescriptionCode
_mapDescriptionCode
sortDescriptionCode
_is_sortedDescriptionCode
Methods description
add_mappercode    nextTop
 Title   : add_mapper
Usage : $obj->add_mapper($mapper)
Function: Pushes one Bio::Coordinate::MapperI into the list of mappers.
Sets _is_sorted() to false.
Example :
Returns : 1 when succeeds, 0 for failure.
Args : mapper object
mapperscodeprevnextTop
 Title   : mappers
Usage : $obj->mappers();
Function: Returns or sets a list of mappers.
Example :
Returns : array of mappers
Args : array of mappers
each_mappercodeprevnextTop
 Title   : each_mapper
Usage : $obj->each_mapper();
Function: Returns a list of mappers.
Example :
Returns : list of mappers
Args : none
mapper_countcodeprevnextTop
 Title   : mapper_count
Usage : my $count = $collection->mapper_count;
Function: Get the count of the number of mappers stored
in this collection
Example :
Returns : integer
Args : none
swapcodeprevnextTop
 Title   : swap
Usage : $obj->swap;
Function: Swap the direction of mapping;input <-> output
Example :
Returns : 1
Args :
testcodeprevnextTop
 Title   : test
Usage : $obj->test;
Function: test that both components of all pairs are of the same length.
Ran automatically.
Example :
Returns : boolean
Args :
mapcodeprevnextTop
 Title   : map
Usage : $newpos = $obj->map($pos);
Function: Map the location from the input coordinate system
to a new value in the output coordinate system.
Example :
Returns : new value in the output coordinate system
Args : integer
_mapcodeprevnextTop
 Title   : _map
Usage : $newpos = $obj->_map($simpleloc);
Function: Internal method that does the actual mapping. Called multiple times
by map() if the location to be mapped is a split location
Example : Returns : new location in the output coordinate system or undef Args : Bio::Location::Simple
sortcodeprevnextTop
 Title   : sort
Usage : $obj->sort;
Function: Sort function so that all mappings are sorted by
input coordinate start
Example :
Returns : 1
Args :
_is_sortedcodeprevnextTop
 Title   : _is_sorted
Usage : $newpos = $obj->_is_sorted;
Function: toggle for whether the (internal) coodinate mapper data are sorted
Example :
Returns : boolean
Args : boolean
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

    $self->{'_mappers'} = [];

    my($in, $out, $strict, $mappers, $return_match) =
	$self->_rearrange([qw(IN
                              OUT
                              STRICT
                              MAPPERS
                              RETURN_MATCH
			     )],
			 @args);

    $in  && $self->in($in);
    $out  && $self->out($out);
    $mappers && $self->mappers($mappers);
    $return_match && $self->return_match('return_match');
    return $self; # success - we hope!
}
add_mapperdescriptionprevnextTop
sub add_mapper {
  my ($self,$value) = @_;

  $self->throw("Is not a Bio::Coordinate::MapperI but a [$self]")
      unless defined $value && $value->isa('Bio::Coordinate::MapperI');
  
  # test pair range lengths
$self->warn("Coordinates in pair [". $value . ":" . $value->in->seq_id . "/". $value->out->seq_id . "] are not right.") unless $value->test; $self->_is_sorted(0); push(@{$self->{'_mappers'}},$value);
}
mappersdescriptionprevnextTop
sub mappers {
   my ($self,@args) = @_;

   if (@args) {

       $self->throw("Is not a Bio::Coordinate::MapperI but a [$self]")
	   unless defined $args[0] && $args[0]->isa('Bio::Coordinate::MapperI');
       push(@{$self->{'_mappers'}}, @args);
   }

   return @{$self->{'_mappers'}};
}
each_mapperdescriptionprevnextTop
sub each_mapper {
   my ($self) = @_;
   return @{$self->{'_mappers'}};
}
mapper_countdescriptionprevnextTop
sub mapper_count {
   my $self = shift;
   return scalar @{$self->{'_mappers'} || []};
}
swapdescriptionprevnextTop
sub swap {
   my ($self) = @_;
   use Data::Dumper;

   $self->sort unless $self->_is_sorted;
   map {$_->swap;} @{$self->{'_mappers'}};
   ($self->{'_in_ids'}, $self->{'_out_ids'}) =
       ($self->{'_out_ids'}, $self->{'_in_ids'});
   1;
}
testdescriptionprevnextTop
sub test {
   my ($self) = @_;

   my $res = 1;

   foreach my $mapper ($self->each_mapper) {
       unless( $mapper->test ) {
	   $self->warn("Coordinates in pair [". $mapper . ":" .
		       $mapper->in->seq_id . "/". $mapper->out->seq_id .
		       "] are not right."); 
	   $res = 0;
       }
   }
   $res;
}
mapdescriptionprevnextTop
sub map {
   my ($self,$value) = @_;

   $self->throw("Need to pass me a value.")
       unless defined $value;
   $self->throw("I need a Bio::Location, not [$value]")
       unless $value->isa('Bio::LocationI');
   $self->throw("No coordinate mappers!")
       unless $self->each_mapper;

   $self->sort unless $self->_is_sorted;


   if ($value->isa("Bio::Location::SplitLocationI")) {

       my $result = Bio::Coordinate::Result->new();
       foreach my $loc ( $value->sub_Location(1) ) {

           my $res = $self->_map($loc);
           map { $result->add_sub_Location($_) } $res->each_Location;

       }
       return $result;

   } else {
       return $self->_map($value);
   }
}
_mapdescriptionprevnextTop
sub _map {
   my ($self,$value) = @_;

   my $result = Bio::Coordinate::Result->new(-is_remote=>1);

IDMATCH: {

       # bail out now we if are forcing the use of an ID 
# and it is not in this collection
last IDMATCH if defined $value->seq_id && ! $self->{'_in_ids'}->{$value->seq_id}; foreach my $pair ($self->each_mapper) { # if we are limiting input to a certain ID
next if defined $value->seq_id && $value->seq_id ne $pair->in->seq_id; # if we haven't even reached the start, move on
next if $pair->in->end < $value->start; # if we have over run, break
last if $pair->in->start > $value->end; my $subres = $pair->map($value); $result->add_result($subres); } } $result->seq_id($result->match->seq_id) if $result->match; unless ($result->each_Location) { #build one gap;
my $gap = Bio::Location::Simple->new(-start => $value->start, -end => $value->end, -strand => $value->strand, -location_type => $value->location_type ); $gap->seq_id($value->seq_id) if defined $value->seq_id; bless $gap, 'Bio::Coordinate::Result::Gap'; $result->seq_id($value->seq_id) if defined $value->seq_id; $result->add_sub_Location($gap); } return $result;
}
sortdescriptionprevnextTop
sub sort {
   my ($self) = @_;

   @{$self->{'_mappers'}} = map { $_->[0] }
                            sort { $a->[1] <=> $b->[1] }
                            map { [ $_, $_->in->start] } 
                            @{$self->{'_mappers'}};

   #create hashes for sequence ids
$self->{'_in_ids'} = (); $self->{'_out_ids'} = (); foreach ($self->each_mapper) { $self->{'_in_ids'}->{$_->in->seq_id} = 1; $self->{'_out_ids'}->{$_->out->seq_id} = 1; } $self->_is_sorted(1);
}
_is_sorteddescriptionprevnextTop
sub _is_sorted {
   my ($self,$value) = @_;

   $self->{'_is_sorted'} = 1 if defined $value && $value;
   return $self->{'_is_sorted'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 lists Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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 BugsTop
report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
CONTRIBUTORSTop
Ewan Birney, birney@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _