Bio::SeqFeature Collection
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Summary
Bio::SeqFeature::Collection - A container class for SeqFeatures
suitable for performing operations such as finding features within a
range, that match a certain feature type, etc.
Package variables
No package variables defined.
Included modules
Bio::DB::GFF::Util::Binning
Bio::Location::Simple
Bio::SeqFeature::Generic
DB_File
Storable qw ( freeze thaw )
Inherit
Bio::Root::Root Bio::SeqFeature::CollectionI
Synopsis
  use Bio::SeqFeature::Collection;
use Bio::Location::Simple;
use Bio::Tools::GFF;
use Bio::Root::IO;
use File::Spec;
# let's first input some features
my $gffio = Bio::Tools::GFF->new(-file => File::Spec->catfile
("t","data","myco_sites.gff"),
-gff_version => 2);
my @features = ();
# loop over the input stream
while(my $feature = $gffio->next_feature()) {
# do something with feature
push @features, $feature;
}
$gffio->close();
# build the Collection object
my $col = Bio::SeqFeature::Collection->new();
# add these features to the object
my $totaladded = $col->add_features(\@features);
my @subset = $col->features_in_range(-start => 1, -end => 25000, -strand => 1, -contain => 0); # subset should have 18 entries for this dataset print "size is ", scalar @subset, "\n"; @subset = $col->features_in_range(-range => Bio::Location::Simple->new (-start => 70000, -end => 150000, -strand => -1), -contain => 1, -strandmatch => 'strong'); # subset should have 22 entries for this dataset print "size is ", scalar @subset, "\n"; print "total number of features in collection is ", $col->feature_count(),"\n";
Description
This object will efficiently allow one for query subsets of ranges
within a large collection of sequence features (in fact the objects
just have to be Bio::RangeI compliant). This is done by the creation
of bins which are stored in order in a B-Tree data structure as
provided by the DB_File interface to the Berkeley DB.
This is based on work done by Lincoln for storage in a mysql instance
- this is intended to be an embedded in-memory implementation for
easily querying for subsets of a large range set.
Collections can be made persistent by keeping the indexfile and
passing in the -keep flag like this:
  my $collection = Bio::SeqFeature::Collection->new(-keep => 1,
-file => 'col.idx');
$collaction->add_features(\@features);
undef $collection;
# To reuse this collection, next time you initialize a Collection object # specify the filename and the index will be reused. $collection = Bio::SeqFeature::Collection->new(-keep => 1, -file => 'col.idx');
Methods
newDescriptionCode
add_featuresDescriptionCode
features_in_rangeDescriptionCode
remove_featuresDescriptionCode
get_all_featuresDescriptionCode
min_binDescriptionCode
max_binDescriptionCode
feature_countDescriptionCode
indexfileDescriptionCode
keepDescriptionCode
_compare
No description
Code
feature_freeze
No description
Code
_remove_cleanup_methods
No description
Code
feature_thaw
No description
Code
DESTROY
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::SeqFeature::Collection->new();
Function: Builds a new Bio::SeqFeature::Collection object
Returns : Bio::SeqFeature::Collection
Args :
-minbin minimum value to use for binning (default is 100,000,000) -maxbin maximum value to use for binning (default is 1,000) -file filename to store/read the BTREE from rather than an in-memory structure (default is false and in-memory). -keep boolean, will not remove index file on object destruction. -features Array ref of features to add initially
add_featurescodeprevnextTop
 Title   : add_features
Usage : $collection->add_features(\@features);
Function:
Returns : number of features added
Args : arrayref of Bio::SeqFeatureI objects to index
features_in_rangecodeprevnextTop
 Title   : features_in_range
Usage : my @features = $collection->features_in_range($range)
Function: Retrieves a list of features which were contained or overlap the
the requested range (see Args for way to specify overlap or
only those containe)d
Returns : List of Bio::SeqFeatureI objects
Args : -range => Bio::RangeI object defining range to search,
OR
-start => start,
-end => end,
-strand => strand
-contain => boolean - true if feature must be completely contained with range OR false if should include features that simply overlap the range. Default: true. -strandmatch => 'strong', ranges must have the same strand 'weak', ranges must have the same strand or no strand 'ignore', ignore strand information Default. 'ignore'.
remove_featurescodeprevnextTop
 Title   : remove_features
Usage : $collection->remove_features(\@array)
Function: Removes the requested sequence features (based on features
which have the same location)
Returns : Number of features removed
Args : Arrayref of Bio::RangeI objects
get_all_featurescodeprevnextTop
 Title   : get_all_features
Usage : my @f = $col->get_all_features()
Function: Return all the features stored in this collection (Could be large)
Returns : Array of Bio::RangeI objects
Args : None
min_bincodeprevnextTop
 Title   : min_bin
Usage : my $minbin= $self->min_bin;
Function: Get/Set the minimum value to use for binning
Returns : integer
Args : [optional] minimum bin value
max_bincodeprevnextTop
 Title   : max_bin
Usage : my $maxbin= $self->max_bin;
Function: Get/Set the maximum value to use for binning
Returns : integer
Args : [optional] maximum bin value
feature_countcodeprevnextTop
 Title   : feature_count
Usage : my $c = $col->feature_count()
Function: Retrieve the total number of features in the collection
Returns : integer
Args : none
indexfilecodeprevnextTop
 Title   : indexfile
Usage : $obj->indexfile($newval)
Function: Get/set the filename where index is kept
Returns : value of indexfile (a filename string)
Args : on set, new value (a filename string )
keepcodeprevnextTop
 Title   : keep
Usage : $obj->keep($newval)
Function: Get/set boolean flag to keep the indexfile after
exiting program
Example :
Returns : value of keep (boolean)
Args : on set, new value (boolean)
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($maxbin,$minbin, $file, $keep,
      $features) = $self->_rearrange([qw(MAXBIN MINBIN FILE KEEP
					 FEATURES)],@args);

  defined $maxbin && $self->max_bin($maxbin);
  defined $minbin && $self->min_bin($minbin);

  defined $features &&  $self->add_features($features);
  $DB_BTREE->{'flags'} = R_DUP ;
  $DB_BTREE->{'compare'} =\& _compare;
  $self->{'_btreehash'} = {};
  if( $file ) {
      $self->debug("using file $file");
      $self->indexfile($file);
  }
  $self->keep($keep);
  $self->{'_btree'} = tie %{$self->{'_btreehash'}},
  'DB_File', $self->indexfile, O_RDWR|O_CREAT, 0640, $DB_BTREE;
  $self->{'_btree'} || $self->throw("Unable to tie DB_File handle");
  return $self;
}
add_featuresdescriptionprevnextTop
sub add_features {
   my ($self,$feats) = @_;
   if( ref($feats) !~ /ARRAY/i ) {
       $self->warn("Must provide a valid Array reference to add_features");
       return 0;
   }
   my $count = 0;
   foreach my $f ( @$feats ) {
       if( ! $f || ! ref($f) || ! $f->isa('Bio::RangeI') ) {
	   $self->warn("Must provide valid Bio::RangeI objects to add_features, skipping object '$f'\n");
	   next;
       }
       my $bin = bin($f->start,$f->end,$self->min_bin);
       my $serialized = &feature_freeze($f);
       $self->{'_btree'}->put($bin,$serialized);
       if( $f->isa('Bio::SeqFeature::Generic') ) {
	   $self->debug( "$bin for ". $f->location->to_FTstring(). " matches ".$#{$self->{'_features'}}. "\n");
       }
       $count++;
   }
   return $count;
}
features_in_rangedescriptionprevnextTop
sub features_in_range {
   my $self = shift;
   my (@args) = @_;
   my ($range, $contain, $strandmatch,$start,$end,$strand);
   if( @args == 1 ) {
       $range = shift @args;
   } else {
       ($start,$end,$strand,$range,
	$contain,$strandmatch) = $self->_rearrange([qw(START END
						       STRAND
						       RANGE CONTAIN
						       STRANDMATCH)],
						   @args);
       $contain = 1 unless defined $contain;
   }
   $strand = 1 unless defined $strand;
   if( $strand !~ /^([\-\+])$/ &&
       $strand !~ /^[\-\+]?1$/ ) {
       $self->warn("must provide a valid numeric or +/- for strand");
       return ();
   }
   if( defined $1 ) { $strand .= 1; }

   if( !defined $start && !defined $end ) {
       if( ! defined $range || !ref($range) || ! $range->isa("Bio::RangeI") )
       {
	   $self->warn("Must defined a valid Range for the method feature_in_range");
	   return ();
       }
       ($start,$end,$strand) = ($range->start,$range->end,$range->strand);
   }
   my $r = Bio::Location::Simple->new(-start => $start,
				     -end   => $end,
				     -strand => $strand);

   my @features;
   my $maxbin = $self->max_bin;
   my $minbin = $self->min_bin;
   my $tier = $maxbin;
   my ($k,$v,@bins) = ("",undef);
   while ($tier >= $minbin) {
	my ($tier_start,$tier_stop) = (bin_bot($tier,$start),
				       bin_top($tier,$end));
       if( $tier_start == $tier_stop ) {
	   my @vals = $self->{'_btree'}->get_dup($tier_start);
	   if( scalar @vals > 0 ) {
	       push @bins, map { thaw($_) } @vals;
	   }
       } else {	
	   $k = $tier_start;
	   my @vals;
	   for( my $rc = $self->{'_btree'}->seq($k,$v,R_CURSOR);
	        $rc == 0;
	        $rc = $self->{'_btree'}->seq($k,$v, R_NEXT) ) {
	       last if( $k > $tier_stop || $k < $tier_start);
	       push @bins, thaw($v);
	   }
       }
       $tier /= 10;
} my %seen = (); foreach my $t ( map { ref($_) } @bins) { next if $seen{$t}++; eval "require $t"; if( $@ ) { $self->warn("Trying to thaw a stored feature $t which does not appear in your Perl library. $@"); next; } } $strandmatch = 'ignore' unless defined $strandmatch; return ( $contain ) ? grep { $r->contains($_,$strandmatch) } @bins : grep { $r->overlaps($_,$strandmatch)} @bins;
}
remove_featuresdescriptionprevnextTop
sub remove_features {
   my ($self,$feats) = @_;
   if( ref($feats) !~ /ARRAY/i ) {
       $self->warn("Must provide a valid Array reference to remove_features");
       return 0;
   }
   my $countprocessed = 0;

   foreach my $f ( @$feats ) {
       next if ! ref($f) || ! $f->isa('Bio::RangeI');
       my $bin = bin($f->start,$f->end,$self->min_bin);
       my @vals = $self->{'_btree'}->get_dup($bin);
       my $vcount = scalar @vals;

       foreach my $v ( @vals )  {
	   # Once we have uniquely identifiable field
# I think it will work better.
if( $v eq &feature_freeze($f) ) { $self->{'_btree'}->del_dup($bin,$v); $vcount--; $countprocessed++; } } if( $vcount == 0 ) { $self->{'_btree'}->del($bin); } } $countprocessed;
}
get_all_featuresdescriptionprevnextTop
sub get_all_features {
   my ($self) = @_;
   my @features;
   my ($key,$value);
   for (my $status = $self->{'_btree'}->seq($key, $value, R_FIRST) ;
	$status == 0 ;
	$status = $self->{'_btree'}->seq($key, $value, R_NEXT) )
   {   next unless defined $value;
       push @features, &thaw($value);
   }
   if( scalar @features !=  $self->feature_count() ) {
       $self->warn("feature count does not match actual count\n");
   }
   return @features;
}
min_bindescriptionprevnextTop
sub min_bin {
  my ($self,$min) = @_;
  if( defined $min ) {
      $self->{'_min_bin'} = $min;
  }
  return $self->{'_min_bin'}  || MIN_BIN;
}
max_bindescriptionprevnextTop
sub max_bin {
  my ($self,$max) = @_;
  if( defined $max ) {
      $self->{'_max_bin'} = $max;
  }
  return $self->{'max_bin'} || MAX_BIN;
}
feature_countdescriptionprevnextTop
sub feature_count {
    my $self = shift;
    my $count = 0;
    for ( keys %{$self->{'_btreehash'}} ) {
	my $v = $self->{'_btreehash'}->{$_};
	next unless defined  $v;
	$count++;
    }
    $count;
}
indexfiledescriptionprevnextTop
sub indexfile {
    my $self = shift;

    return $self->{'indexfile'} = shift if @_;
    return $self->{'indexfile'};
}
keepdescriptionprevnextTop
sub keep {
    my $self = shift;

    return $self->{'keep'} = shift if @_;
    return $self->{'keep'};
}
_comparedescriptionprevnextTop
sub _compare {
    if( defined $_[0] && ! defined $_[1]) {
	return -1;
    } elsif ( defined $_[1] && ! defined $_[0]) {
	return 1;
    }
    $_[0] <=> $_[1];
}
feature_freezedescriptionprevnextTop
sub feature_freeze {
    my $obj = shift;
    _remove_cleanup_methods($obj);
    return freeze($obj);
}
_remove_cleanup_methodsdescriptionprevnextTop
sub _remove_cleanup_methods {
    my $obj = shift;
    
    # we have to remove any cleanup methods here for Storable
for my $funcref ( $obj->_cleanup_methods ) { $obj->_unregister_for_cleanup($funcref); } # ... and the same for any contained features; hopefully any implementations
# adhere to implementing Bio::SeqFeatureI::sub_SeqFeature
for my $contained ($obj->sub_SeqFeature) { _remove_cleanup_methods($contained); } 1;
}
feature_thawdescriptionprevnextTop
sub feature_thaw {
    return thaw(shift);
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self = shift;
    $self->{'_btree'} = undef;
    untie(%{$self->{'_btreehash'}});
    if( ! $self->keep && $self->indexfile ) {
        my $f = $self->indexfile;
        $self->debug( "unlinking ".$f. "\n");
        close($f);
        unlink($f);
    }
    $self->SUPER::DESTROY();    
}

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 list. 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
of the bugs and their resolution. Bug reports can be submitted via
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
CONTRIBUTORSTop
Using code and strategy developed by Lincoln Stein (lstein@cshl.org)
in Bio::DB::GFF implementation. Credit also to Lincoln for suggesting
using Storable to serialize features rather than my previous implementation
which kept the features in memory.
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _