Bio::SeqFeature::Collection(3p)

NAME
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.

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');

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 - Jason Stajich
Email jason@bioperl.org

CONTRIBUTORS
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.

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  new
 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_features
 Title   : add_features
 Usage   : $collection->add_features(\@features);
 Function:
 Returns : number of features added
 Args    : arrayref of Bio::SeqFeatureI objects to index

  features_in_range
 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_features
 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_features
 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_bin
 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_bin
 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_count
 Title   : feature_count
 Usage   : my $c = $col->feature_count()
 Function: Retrieve the total number of features in the collection
 Returns : integer
 Args    : none

  indexfile
 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 )

  keep
 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)