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. All features are held in memory even if the -usefile flag is provided.
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Using code and strategy developed by Lincoln Stein (lstein@cshl.org) in Bio::DB::GFF implementation.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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) -usefile boolean to use a file to store BTREE rather than an in-memory structure (default is false or in-memory). -features Array ref of features to add initially
Title : add_features Usage : $collection->add_features(\@features); Function: Returns : number of features added Args : arrayref of Bio::SeqFeatureI objects to index
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'.
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
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
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
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
Title : feature_count Usage : my $c = $col->feature_count() Function: Retrieve the total number of features in the collection Returns : integer Args : none
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.