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Bio::SeqFeature::Collection.3pm

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 quering for subsets of a large range set.

Collections can be made persistant 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:

   http://bugzilla.open-bio.org/
 
 

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)