Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages


home | help
Bio::SeqFeature::ColleUsernContributed Perl DocuBio::SeqFeature::Collection(3)

       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;
	 use File::Spec;
	 # let's first input some features
	 my $gffio = Bio::Tools::GFF->new(-file	=> File::Spec->catfile
					-gff_version =>	2);
	 my @features =	();
	 # loop	over the input stream
	 while(my $feature = $gffio->next_feature()) {
	     # do something with feature
	     push @features, $feature;
	 # 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 ",

       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');
	 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');

   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.			- General discussion	- About	the mailing lists

       Please direct usage questions or	support	issues to the mailing list:

       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

AUTHOR - Jason Stajich

       Using code and strategy developed by Lincoln Stein ( 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 _

	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

	Title	: add_features
	Usage	: $collection->add_features(\@features);
	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,
		  -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

	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 )

	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)

perl v5.32.1			  2019-12-07	Bio::SeqFeature::Collection(3)


Want to link to this manual page? Use this URL:

home | help