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. use Bio::SeqFeature::Collection; use Bio::Location::Simple; use Bio::Tools::GFF; use Bio::Root::IO; # let's first input some features my $gffio = Bio::Tools::GFF->new(-file => Bio::Root::IO->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 = new Bio::SeqFeature::Collection(); # 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"; 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 = new Bio::SeqFeature::Collection(-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 = new Bio::SeqFeature::Collection(-keep => 1, -file => 'col.idx');

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/MailList.shtml - About the mailing lists

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.bioperl.org/ Email jason@bioperl.org 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. The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::SeqFeature::Collection(); 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)