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;
# 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";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 = 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');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 listsReporting 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 = 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 initiallyadd_features
Title : add_features
Usage : $collection->add_features(\@features);
Function:
Returns : number of features added
Args : arrayref of Bio::SeqFeatureI objects to indexfeatures_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 objectsget_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 : Nonemin_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 valuemax_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 valuefeature_count
Title : feature_count
Usage : my $c = $col->feature_count()
Function: Retrieve the total number of features in the collection
Returns : integer
Args : noneindexfile
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)