package Bio::DB::SeqFeature::Store;
=head1 NAME
Bio::DB::SeqFeature::Store -- Storage and retrieval of sequence annotation data
=head1 SYNOPSIS
use Bio::DB::SeqFeature::Store;
# Open the feature database
my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql',
-dsn => 'dbi:mysql:test',
-create => 1 );
# Get a feature from somewhere
my $feature = Bio::SeqFeature::Generic->new(...);
# Store it
$db->store($feature) or die "Couldn't store!";
# If absent, a primary ID is added to the feature when it is stored in the
# database. Retrieve the primary ID
my $id = $feature->primary_id;
# Get the feature back out
my $feature = $db->fetch($id);
# .... which is identical to
my $feature = $db->get_feature_by_primary_id($id);
# Change the feature and update it
$f->start(100);
$db->store($f) or die "Couldn't update!";
# Get all features at once
my @features = $db->features( );
# Retrieve multiple features by primary id
my @features = $db->fetch_many(@list_of_ids);
# ...by name
@features = $db->get_features_by_name('ZK909');
# ...by alias
@features = $db->get_features_by_alias('sma-3');
# ...by type
@features = $db->get_features_by_type('gene');
# ...by location
@features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000);
# ...by attribute
@features = $db->get_features_by_attribute({description => 'protein kinase'})
# ...by the GFF "Note" field
@result_list = $db->search_notes('kinase');
# ...by arbitrary combinations of selectors
@features = $db->features(-name => $name,
-type => $types,
-seq_id => $seqid,
-start => $start,
-end => $end,
-attributes => $attributes);
# Loop through the features using an iterator
my $iterator = $db->get_seq_stream(-name => $name,
-type => $types,
-seq_id => $seqid,
-start => $start,
-end => $end,
-attributes => $attributes);
while (my $feature = $iterator->next_seq) {
# do something with the feature
}
# ...limiting the search to a particular region
my $segment = $db->segment('Chr1',5000=>6000);
my @features = $segment->features(-type=>['mRNA','match']);
# Getting coverage statistics across a region
my $summary = $db->feature_summary('Chr1',10_000=>1_110_000);
my ($bins) = $summary->get_tag_values('coverage');
my $first_bin = $bins->[0];
# Getting & storing sequence information
# Warning: this returns a string, and not a PrimarySeq object
$db->insert_sequence('Chr1','GATCCCCCGGGATTCCAAAA...');
my $sequence = $db->fetch_sequence('Chr1',5000=>6000);
# What feature types are defined in the database?
my @types = $db->types;
# Create a new feature in the database
my $feature = $db->new_feature(-primary_tag => 'mRNA',
-seq_id => 'chr3',
-start => 10000,
-end => 11000);
# Load an entire GFF3 file, using the GFF3 loader...
my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store => $db,
-verbose => 1,
-fast => 1);
$loader->load('./my_genome.gff3');
=head1 DESCRIPTION
Bio::DB::SeqFeature::Store implements the Bio::SeqFeature::CollectionI
interface to allow you to persistently store Bio::SeqFeatureI objects
in a database and to later to retrieve them by a variety of
searches. This module is similar to the older Bio::DB::GFF module,
with the following differences:
=over 4
=item 1.
No limitation on Bio::SeqFeatureI implementations
Unlike Bio::DB::GFF, Bio::DB::SeqFeature::Store works with
any Bio::SeqFeatureI object.
=item 2.
No limitation on nesting of features & subfeatures
Bio::DB::GFF is limited to features that have at most one
level of subfeature. Bio::DB::SeqFeature::Store can work with features
that have unlimited levels of nesting.
=item 3.
No aggregators
The aggregator architecture, which was necessary to impose order on
the GFF2 files that Bio::DB::GFF works with, does not apply to
Bio::DB::SeqFeature::Store. It is intended to store features that obey
well-defined ontologies, such as the Sequence Ontology
(http://song.sourceforge.net).
=item 4.
No relative locations
All locations defined by this module are relative to an absolute
sequence ID, unlike Bio::DB::GFF which allows you to define the
location of one feature relative to another.
=back
We'll discuss major concepts in Bio::DB::SeqFeature::Store and then
describe how to use the module.
=head2 Adaptors
Bio::DB::SeqFeature::Store is designed to work with a variety of
storage back ends called "adaptors." Adaptors are subclasses of
Bio::DB::SeqFeature::Store and provide the interface between the
store() and fetch() methods and the physical database. Currently the
number of adaptors is quite limited, but the number will grow soon.
=over 4
=item memory
An implementation that stores all data in memory. This is useful for
small data sets of no more than 10,000 features (more or less,
depending on system memory).
=item DBI::mysql
A full-featured implementation on top of the MySQL relational database
system.
=item berkeleydb
A full-feature implementation that runs on top of the BerkeleyDB
database. See L<Bio::DB::SeqFeature::Store::berkeleydb>.
=back
If you do not explicitly specify the adaptor, then DBI::mysql will be
used by default.
=head2 Serializers
When Bio::DB::SeqFeature::Store stores a Bio::SeqFeatureI object into
the database, it serializes it into binary or text form. When it later
fetches the feature from the database, it unserializes it. Two
serializers are available: Recent versions of
=over 4
=item Storable
This is a fast binary serializer. It is available in Perl versions
5.8.7 and higher and is used when available.
=item Data::Dumper
This is a slow text serializer that is available in Perl 5.8.0 and
higher. It is used when Storable is unavailable.
=back
If you do not specify the serializer, then Storable will be used if
available; otherwise Data::Dumper.
=head2 Loaders and Normalized Features
The Bio::DB::SeqFeature::Store::GFF3Loader parses a GFF3-format file
and loads the annotations and sequence data into the database of your
choice. The script bp_seqfeature_load.pl (found in the
scripts/Bio-SeqFeature-Store/ subdirectory) is a thin front end to the
GFF3Loader. Other loaders may be written later.
Although Bio::DB::SeqFeature::Store should work with any
Bio::SeqFeatureI object, there are some disadvantages to using
Bio::SeqFeature::Generic and other vanilla implementations. The major
issue is that if two vanilla features share the same subfeature
(e.g. two transcripts sharing an exon), the shared subfeature will be
cloned when stored into the database.
The special-purpose L<Bio::DB::SeqFeature> class is able to normalize
its subfeatures in the database, so that shared subfeatures are stored
only once. This minimizes wasted storage space. In addition, when
in-memory caching is turned on, each shared subfeature will usually
occupy only a single memory location upon restoration.
=cut
use strict;
use warnings;
use base 'Bio::SeqFeature::CollectionI';
use Carp 'croak';
use Bio::DB::GFF::Util::Rearrange;
use Bio::DB::SeqFeature::Segment;
use Scalar::Util 'blessed';
# this probably shouldn't be here
use Bio::DB::SeqFeature;
*dna = *get_dna = *get_sequence = \&fetch_sequence;
*get_SeqFeatures = \&fetch_SeqFeatures;
# local version
sub api_version { 1.2 }
=head1 Methods for Connecting and Initializating a Database
## TODO: http://iowg.brcdevel.org/gff3.html#a_fasta is a dead link
=head2 new
Title : new
Usage : $db = Bio::DB::SeqFeature::Store->new(@options)
Function: connect to a database
Returns : A descendent of Bio::DB::Seqfeature::Store
Args : several - see below
Status : public
This class method creates a new database connection. The following
-name=E<gt>$value arguments are accepted:
Name Value
---- -----
-adaptor The name of the Adaptor class (default DBI::mysql)
-serializer The name of the serializer class (default Storable)
-index_subfeatures Whether or not to make subfeatures searchable
(default false)
-cache Activate LRU caching feature -- size of cache
-compress Compresses features before storing them in database
using Compress::Zlib
-create (Re)initialize the database.
The B<-index_subfeatures> argument, if true, tells the module to
create indexes for a feature and all its subfeatures (and its
subfeatures' subfeatures). Indexing subfeatures means that you will be
able to search for the gene, its mRNA subfeatures and the exons inside
each mRNA. It also means when you search the database for all features
contained within a particular location, you will get the gene, the
mRNAs and all the exons as individual objects as well as subfeatures
of each other. NOTE: this option is only honored when working with a
normalized feature class such as Bio::DB::SeqFeature.
The B<-cache> argument, if true, tells the module to try to create a
LRU (least-recently-used) object cache using the Tie::Cacher
module. Caching will cause two objects that share the same primary_id
to (often, but not always) share the same memory location, and may
improve performance modestly. The argument is taken as the desired
size for the cache. If you pass "1" as the cache value, a reasonable
default cache size will be chosen. Caching requires the Tie::Cacher
module to be installed. If the module is not installed, then caching
will silently be disabled.
The B<-compress> argument, if true, will cause the feature data to be
compressed before storing it. This will make the database somewhat
smaller at the cost of decreasing performance.
The B<-create> argument, if true, will either initialize or
reinitialize the database. It is needed the first time a database is
used.
The new() method of individual adaptors recognize additional
arguments. The default DBI::mysql adaptor recognizes the following
ones:
Name Value
---- -----
-dsn DBI data source (default dbi:mysql:test)
-autoindex A flag that controls whether or not to update
all search indexes whenever a feature is stored
or updated (default true).
-namespace A string that will be used to qualify each table,
thereby allowing you to store several independent
sequence feature databases in a single Mysql
database.
-dumpdir The path to a temporary directory that will be
used during "fast" loading. See
L<Bio::DB::SeqFeature::Store::GFF3Loader> for a
description of this. Default is the current
directory.
-write Make the database writable (implied by -create)
-fasta Provide an alternative DNA accessor object or path.
By default the database will store DNA sequences internally. However,
you may override this behavior by passing either a path to a FASTA
file, or any Perl object that recognizes the seq($seqid,$start,$end)
method. In the former case, the FASTA path will be passed to
Bio::DB::Fasta, possibly causing an index to be constructed. Suitable
examples of the latter type of object include the Bio::DB::Sam and
Bio::DB::Sam::Fai classes.
=cut
###
# object constructor
#
sub new {
my $self = shift;
my ($adaptor,$serializer,$index_subfeatures,$cache,$compress,$debug,$create,$fasta,$args);
if (@_ == 1) {
$args = {DSN => shift}
}
else {
($adaptor,$serializer,$index_subfeatures,$cache,$compress,$debug,$create,$fasta,$args) =
rearrange(['ADAPTOR',
'SERIALIZER',
'INDEX_SUBFEATURES',
'CACHE',
'COMPRESS',
'DEBUG',
'CREATE',
'FASTA',
],@_);
}
$adaptor ||= 'DBI::mysql';
$args->{WRITE}++ if $create;
$args->{CREATE}++ if $create;
my $class = "Bio::DB::SeqFeature::Store::$adaptor";
eval "require $class " or croak $@;
$cache &&= eval "require Tie::Cacher; 1";
my $obj = $class->new_instance();
$obj->debug($debug) if defined $debug;
$obj->init($args);
$obj->init_cache($cache) if $cache;
$obj->do_compress($compress);
$obj->serializer($serializer) if defined $serializer;
$obj->index_subfeatures($index_subfeatures) if defined $index_subfeatures;
$obj->seqfeature_class('Bio::DB::SeqFeature');
$obj->set_dna_accessor($fasta) if defined $fasta;
$obj->post_init($args);
$obj;
}
=head2 init_database
Title : init_database
Usage : $db->init_database([$erase_flag])
Function: initialize a database
Returns : true
Args : (optional) flag to erase current data
Status : public
Call this after Bio::DB::SeqFeature::Store-E<gt>new() to initialize a
new database. In the case of a DBI database, this method installs the
schema but does B<not> create the database. You have to do this
offline using the appropriate command-line tool. In the case of the
"berkeleydb" adaptor, this creates an empty BTREE database.
If there is any data already in the database, init_database() called
with no arguments will have no effect. To permanently erase the data
already there and prepare to receive a fresh set of data, pass a true
argument.
=cut
###
# wipe database clean and reinstall schema
#
sub init_database {
my $self = shift;
$self->_init_database(@_);
}
=head2 post_init
This method is invoked after init_database for use by certain adaptors
(currently only the memory adaptor) to do automatic data loading after
initialization. It is passed a copy of the init_database() args.
=cut
sub post_init { }
=head2 add_features
Title : add_features
Usage : $success = $db->add_features(\@features)
Function: store one or more features into the database
Returns : true if successful
Args : array reference of Bio::SeqFeatureI objects
Status : public
=cut
sub add_features {
my ($self, $feats) = @_;
my $result = $self->store_and_cache(1, @$feats);
}
=head2 store
Title : store
Usage : $success = $db->store(@features)
Function: store one or more features into the database
Returns : true if successful
Args : list of Bio::SeqFeatureI objects
Status : public
This method stores a list of features into the database. Each feature
is updated so that its primary_id becomes the primary ID of the
serialized feature stored in the database. If all features were
successfully stored, the method returns true. In the DBI
implementation, the store is performed as a single transaction and the
transaction is rolled back if one or more store operations failed.
In most cases, you should let the database assign the primary id. If
the object you store already has a primary_id, then the ID must adhere
to the datatype expected by the adaptor: an integer in the
case of the various DB adaptors, and a string in the case of the
memory and berkeley adaptors.
You can find out what the primary ID of the feature has become by
calling the feature's primary_id() method:
$db->store($my_feature) or die "Oh darn";
my $id = $my_feature->primary_id;
If the feature contains subfeatures, they will all be stored
recursively. In the case of Bio::DB::SeqFeature and
Bio::DB::SeqFeature::Store::NormalizedFeature, the subfeatures will be
stored in a normalized way so that each subfeature appears just once
in the database.
Subfeatures will be indexed for separate retrieval based on the
current value of index_subfeatures().
If you call store() with one or more features that already have valid
primary_ids, then any existing objects will be B<replaced>. Note that
when using normalized features such as Bio::DB::SeqFeature, the
subfeatures are not recursively updated when you update the parent
feature. You must manually update each subfeatures that has changed.
=cut
###
# store one or more Bio::SeqFeatureI objects
# if they already have a primary_id will replace into the database
# otherwise will insert and primary_id will be added
#
# this version stores the object and flags it to be indexed
# for search via attributes, name, type or location
sub store {
my ($self, @feats) = @_;
for my $feat (@feats) {
if ( (not ref $feat) || (not $feat->isa('Bio::SeqFeatureI')) ) {
die "Cannot store non-Bio::SeqFeatureI object '$feat'\n";
}
}
my $result = $self->store_and_cache(1,@feats);
}
=head2 store_noindex
Title : store_noindex
Usage : $success = $db->store_noindex(@features)
Function: store one or more features into the database without indexing
Returns : true if successful
Args : list of Bio::SeqFeatureI objects
Status : public
This method stores a list of features into the database but does not
make them searchable. The only way to access the features is via their
primary IDs. This method is ordinarily only used internally to store
subfeatures that are not indexed.
=cut
# this version stores the object and flags it so that it is
# not searchable via attributes, name, type or location
# (typically used only for subfeatures)
sub store_noindex {
my $self = shift;
$self->store_and_cache(0,@_);
}
=head2 no_blobs
Title : no_blobs
Usage : $db->no_blobs(1);
Function: decide if objects should be stored in the database as blobs.
Returns : boolean (default false)
Args : boolean (true to no longer store objects; when the corresponding
feature is retrieved it will instead be a minimal representation of
the object that was stored, as some simple Bio::SeqFeatureI object)
Status : dubious (new)
This method saves lots of space in the database, which may in turn lead to large
performance increases in extreme cases (over 7 million features in the db).
=cut
sub no_blobs {
my $self = shift;
if (@_) { $self->{no_blobs} = shift }
return $self->{no_blobs} || 0;
}
=head2 new_feature
Title : new_feature
Usage : $feature = $db->new_feature(@args)
Function: create a new Bio::DB::SeqFeature object in the database
Returns : the new seqfeature
Args : see below
Status : public
This method creates and stores a new Bio::SeqFeatureI object using the
specialized Bio::DB::SeqFeature class. This class is able to store its
subfeatures in a normalized fashion, allowing subfeatures to be shared
among multiple parents (e.g. multiple exons shared among several
mRNAs).
The arguments are the same as for Bio::DB::SeqFeature-E<gt>new(), which in
turn are similar to Bio::SeqFeature::Generic-E<gt>new() and
Bio::Graphics::Feature-E<gt>new(). The most important difference is the
B<-index> option, which controls whether the feature will be indexed
for retrieval (default is true). Ordinarily, you would only want to
turn indexing off when creating subfeatures, because features stored
without indexes will only be reachable via their primary IDs or their
parents.
Arguments are as follows:
-seq_id the reference sequence
-start the start position of the feature
-end the stop position of the feature
-display_name the feature name (returned by seqname)
-primary_tag the feature type (returned by primary_tag)
-source the source tag
-score the feature score (for GFF compatibility)
-desc a description of the feature
-segments a list of subfeatures (see Bio::Graphics::Feature)
-subtype the type to use when creating subfeatures
-strand the strand of the feature (one of -1, 0 or +1)
-phase the phase of the feature (0..2)
-url a URL to link to when rendered with Bio::Graphics
-attributes a hashref of tag value attributes, in which the key is the tag
and the value is an array reference of values
-index index this feature if true
Aliases:
-id an alias for -display_name
-seqname an alias for -display_name
-display_id an alias for -display_name
-name an alias for -display_name
-stop an alias for end
-type an alias for primary_tag
You can change the seqfeature implementation generated by new() by
passing the name of the desired seqfeature class to
$db-E<gt>seqfeature_class().
=cut
sub new_feature {
my $self = shift;
return $self->seqfeature_class->new(-store=>$self,@_);
}
=head2 delete
Title : delete
Usage : $success = $db->delete(@features)
Function: delete a list of feature from the database
Returns : true if successful
Args : list of features
Status : public
This method looks up the primary IDs from a list of features and
deletes them from the database, returning true if all deletions are
successful.
WARNING: The current DBI::mysql implementation has some issues that
need to be resolved, namely (1) normalized subfeatures are NOT
recursively deleted; and (2) the deletions are not performed in a
transaction.
=cut
sub delete {
my $self = shift;
my $success = 1;
for my $object (@_) {
my $id = $object->primary_id;
if ( not defined $id ) {
warn "Could not delete feature without primary_id: $object";
$success = 0;
next;
}
my $result = $self->_deleteid($id);
warn "Could not delete feature with id=$id" unless $result;
$success &&= $result;
}
$success;
}
=head2 fetch / get_feature_by_id / get_feature_by_primary_id
Title : fetch
get_feature_by_id
get_feature_by_primary_id
Usage : $feature = $db->fetch($primary_id)
Function: fetch a feature from the database using its primary ID
Returns : a feature
Args : primary ID of desired feature
Status : public
This method returns a previously-stored feature from the database
using its primary ID. If the primary ID is invalid, it returns undef.
Use fetch_many() to rapidly retrieve multiple features.
=cut
###
# Fetch a Bio::SeqFeatureI from database using its primary_id
#
sub fetch {
my $self = shift;
@_ or croak "usage: fetch(\$primary_id)";
my $primary_id = shift;
if (my $cache = $self->cache()) {
return $cache->fetch($primary_id) if $cache->exists($primary_id);
my $object = $self->_fetch($primary_id);
$cache->store($primary_id,$object);
return $object;
}
else {
return $self->_fetch($primary_id);
}
}
*get_feature_by_id = *get_feature_by_primary_id = \&fetch;
=head2 fetch_many
Title : fetch_many
Usage : @features = $db->fetch_many($primary_id,$primary_id,$primary_id...)
Function: fetch many features from the database using their primary ID
Returns : list of features
Args : a list of primary IDs or an array ref of primary IDs
Status : public
Same as fetch() except that you can pass a list of primary IDs or a
ref to an array of IDs.
=cut
###
# Efficiently fetch a series of IDs from the database
# Can pass an array or an array ref
#
sub fetch_many {
my $self = shift;
@_ or croak 'usage: fetch_many($id1,$id2,$id3...)';
my @ids = map {ref($_) ? @$_ : $_} @_ or return;
$self->_fetch_many(@ids);
}
=head2 get_seq_stream
Title : get_seq_stream
Usage : $iterator = $db->get_seq_stream(@args)
Function: return an iterator across all features in the database
Returns : a Bio::DB::SeqFeature::Store::Iterator object
Args : feature filters (optional)
Status : public
When called without any arguments this method will return an iterator
object that will traverse all indexed features in the database. Call
the iterator's next_seq() method to step through them (in no
particular order):
my $iterator = $db->get_seq_stream;
while (my $feature = $iterator->next_seq) {
print $feature->primary_tag,' ',$feature->display_name,"\n";
}
You can select a subset of features by passing a series of filter
arguments. The arguments are identical to those accepted by
$db-E<gt>features().
=cut
###
# Return an iterator across all features that are indexable
#
sub get_seq_stream {
my $self = shift;
$self->_features(-iterator=>1,@_);
}
=head2 get_features_by_name
Title : get_features_by_name
Usage : @features = $db->get_features_by_name($name)
Function: looks up features by their display_name
Returns : a list of matching features
Args : the desired name
Status : public
This method searches the display_name of all features for matches
against the provided name. GLOB style wildcares ("*", "?") are
accepted, but may be slow.
The method returns the list of matches, which may be zero, 1 or more
than one features. Be prepared to receive more than one result, as
display names are not guaranteed to be unique.
For backward compatibility with gbrowse, this method is also known as
get_feature_by_name().
=cut
###
# get_feature_by_name() return 0 or more features using a name lookup
# uses the Bio::DB::GFF API
#
sub get_features_by_name {
my $self = shift;
my ($class,$name,$types,$allow_alias);
if (@_ == 1) { # get_features_by_name('name');
$name = shift;
} else { # get_features_by_name('class'=>'name'), get_feature_by_name(-name=>'name')
($class,$name,$allow_alias,$types) = rearrange([qw(CLASS NAME ALIASES),[qw(TYPE TYPES)]],@_);
}
# hacky workaround for assumption in Bio::DB::GFF that unclassed reference points were of type "Sequence"
undef $class if $class && $class eq 'Sequence';
$self->_features(-name=>$name,-class=>$class,-aliases=>$allow_alias,-type=>$types);
}
=head2 get_feature_by_name
Title : get_feature_by_name
Usage : @features = $db->get_feature_by_name($name)
Function: looks up features by their display_name
Returns : a list of matching features
Args : the desired name
Status : Use get_features_by_name instead.
This method is provided for backward compatibility with gbrowse.
=cut
sub get_feature_by_name { shift->get_features_by_name(@_) }
=head2 get_features_by_alias
Title : get_features_by_alias
Usage : @features = $db->get_features_by_alias($name)
Function: looks up features by their display_name or alias
Returns : a list of matching features
Args : the desired name
Status : public
This method is similar to get_features_by_name() except that it will
also search through the feature aliases. Aliases can be created by
storing features that contain one or more Alias tags. Wildards are
accepted.
=cut
sub get_features_by_alias {
my $self = shift;
my @args = @_;
if (@_ == 1) {
@args = (-name=>shift);
}
push @args,(-aliases=>1);
$self->get_features_by_name(@args);
}
=head2 get_features_by_type
Title : get_features_by_type
Usage : @features = $db->get_features_by_type(@types)
Function: looks up features by their primary_tag
Returns : a list of matching features
Args : list of primary tags
Status : public
This method will return a list of features that have any of the
primary tags given in the argument list. For compatibility with
gbrowse and Bio::DB::GFF, types can be qualified using a colon:
primary_tag:source_tag
in which case only features that match both the primary_tag B<and> the
indicated source_tag will be returned. If the database was loaded from
a GFF3 file, this corresponds to the third and second columns of the
row, in that order.
For example, given the GFF3 lines:
ctg123 geneFinder exon 1300 1500 . + . ID=exon001
ctg123 fgenesH exon 1300 1520 . + . ID=exon002
exon001 and exon002 will be returned by searching for type "exon", but
only exon001 will be returned by searching for type "exon:fgenesH".
=cut
sub get_features_by_type {
my $self = shift;
my @types = @_;
$self->_features(-type=>\@types);
}
=head2 get_features_by_location
Title : get_features_by_location
Usage : @features = $db->get_features_by_location(@args)
Function: looks up features by their location
Returns : a list of matching features
Args : see below
Status : public
This method fetches features based on a location range lookup. You
call it using a positional list of arguments, or a list of
(-argument=E<gt>$value) pairs.
The positional form is as follows:
$db->get_features_by_location($seqid [[,$start,]$end])
The $seqid is the name of the sequence on which the feature resides,
and start and end are optional endpoints for the match. If the
endpoints are missing then any feature on the indicated seqid is
returned.
Examples:
get_features_by_location('chr1'); # all features on chromosome 1
get_features_by_location('chr1',5000); # features between 5000 and the end
get_features_by_location('chr1',5000,8000); # features between 5000 and 8000
Location lookups are overlapping. A feature will be returned if it
partially or completely overlaps the indicated range.
The named argument form gives you more control:
Argument Value
-------- -----
-seq_id The name of the sequence on which the feature resides
-start Start of the range
-end End of the range
-strand Strand of the feature
-range_type Type of range to search over
The B<-strand> argument, if present, can be one of "0" to find
features that are on both strands, "+1" to find only plus strand
features, and "-1" to find only minus strand features. Specifying a
strand of undef is the same as not specifying this argument at all,
and retrieves all features regardless of their strandedness.
The B<-range_type> argument, if present, can be one of "overlaps" (the
default), to find features whose positions overlap the indicated
range, "contains," to find features whose endpoints are completely
contained within the indicated range, and "contained_in" to find
features whose endpoints are both outside the indicated range.
=cut
sub get_features_by_location {
my $self = shift;
my ($seqid,$start,$end,$strand,$rangetype) =
rearrange([['SEQ_ID','SEQID','REF'],'START',['STOP','END'],'STRAND','RANGE_TYPE'],@_);
$self->_features(-seqid=>$seqid,
-start=>$start||undef,
-end=>$end||undef,
-strand=>$strand||undef,
-range_type=>$rangetype);
}
=head2 get_features_by_attribute
Title : get_features_by_attribute
Usage : @features = $db->get_features_by_attribute(@args)
Function: looks up features by their attributes/tags
Returns : a list of matching features
Args : see below
Status : public
This implements a simple tag filter. Pass a list of tag names and
their values. The module will return a list of features whose tag
names and values match. Tag names are case insensitive. If multiple
tag name/value pairs are present, they will be ANDed together. To
match any of a list of values, use an array reference for the value.
Examples:
# return all features whose "function" tag is "GO:0000123"
@features = $db->get_features_by_attribute(function => 'GO:0000123');
# return all features whose "function" tag is "GO:0000123" or "GO:0000555"
@features = $db->get_features_by_attribute(function => ['GO:0000123','GO:0000555']);
# return all features whose "function" tag is "GO:0000123" or "GO:0000555"
# and whose "confirmed" tag is 1
@features = $db->get_features_by_attribute(function => ['GO:0000123','GO:0000555'],
confirmed => 1);
=cut
sub get_features_by_attribute {
my $self = shift;
my %attributes = ref($_[0]) ? %{$_[0]} : @_;
%attributes or $self->throw("Usage: get_feature_by_attribute(attribute_name=>\$attribute_value...)");
$self->_features(-attributes=>\%attributes);
}
###
# features() call -- main query interface
#
=head2 features
Title : features
Usage : @features = $db->features(@args)
Function: generalized query & retrieval interface
Returns : list of features
Args : see below
Status : Public
This is the workhorse for feature query and retrieval. It takes a
series of -name=E<gt>$value arguments filter arguments. Features that
match all the filters are returned.
Argument Value
-------- -----
Location filters:
-seq_id Chromosome, contig or other DNA segment
-seqid Synonym for -seq_id
-ref Synonym for -seqid
-start Start of range
-end End of range
-stop Synonym for -end
-strand Strand
-range_type Type of range match ('overlaps','contains','contained_in')
Name filters:
-name Name of feature (may be a glob expression)
-aliases If true, match aliases as well as display names
-class Archaic argument for backward compatibility.
(-class=>'Clone',-name=>'ABC123') is equivalent
to (-name=>'Clone:ABC123')
Type filters:
-types List of feature types (array reference) or one type (scalar)
-type Synonym for the above
-primary_tag Synonym for the above
-attributes Hashref of attribute=>value pairs as per
get_features_by_attribute(). Multiple alternative values
can be matched by providing an array reference.
-attribute synonym for -attributes
You may also provide features() with a list of scalar values (the
first element of which must B<not> begin with a dash), in which case
it will treat the list as a feature type filter.
Examples:
All features:
@features = $db->features( );
All features on chromosome 1:
@features = $db->features(-seqid=>'Chr1');
All features on chromosome 1 between 5000 and 6000:
@features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000);
All mRNAs on chromosome 1 between 5000 and 6000:
@features = $db->features(-seqid=>'Chr1',-start=>5000,-end=>6000,-types=>'mRNA');
All confirmed mRNAs and repeats on chromosome 1 that overlap the range 5000..6000:
@features = $db->features(-seqid => 'Chr1',-start=>5000,-end=>6000,
-types => ['mRNA','repeat'],
-attributes=> {confirmed=>1}
);
All confirmed mRNAs and repeats on chromosome 1 strictly contained within the range 5000..6000:
@features = $db->features(-seqid => 'Chr1',-start=>5000,-end=>6000,
-types => ['mRNA','repeat'],
-attributes=> {confirmed=>1}
-range_type => 'contained_in',
);
All genes and repeats:
@features = $db->features('gene','repeat_region');
=cut
# documentation of args
# my ($seq_id,$start,$end,$strand,
# $name,$class,$allow_aliases,
# $types,
# $attributes,
# $range_type,
# $iterator,
# ) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'],'STRAND',
# 'NAME','CLASS','ALIASES',
# ['TYPES','TYPE','PRIMARY_TAG'],
# ['ATTRIBUTES','ATTRIBUTE'],
# 'RANGE_TYPE',
# ],@_);
# $range_type ||= 'overlaps';
sub features {
my $self = shift;
my @args;
if (@_ == 0) {
@args = ();
}
elsif ($_[0] !~/^-/) {
my @types = @_;
@args = (-type=>\@types);
} else {
@args = @_;
}
$self->_features(@args);
}
=head2 get_all_features
Title : get_all_features
Usage : @features = $db->get_all_features()
Function: get all feature in the database
Returns : list of features
Args : none
Status : Public
=cut
# for compatibility with Bio::SeqFeature::Collection
sub get_all_features {
shift->features();
}
=head2 seq_ids
Title : seq_ids
Usage : @ids = $db->seq_ids()
Function: Return all sequence IDs contained in database
Returns : list of sequence Ids
Args : none
Status : public
=cut
sub seq_ids {
my $self = shift;
return $self->_seq_ids();
}
=head2 search_attributes
Title : search_attributes
Usage : @result_list = $db->search_attributes("text search string",[$tag1,$tag2...],$limit)
Function: Search attributes for keywords occurring in a text string
Returns : array of results
Args : full text search string, array ref of attribute names, and an optional feature limit
Status : public
Given a search string, this method performs a full-text search of the
specified attributes and returns an array of results. You may pass a
scalar attribute name to search the values of one attribute
(e.g. "Note") or you may pass an array reference to search inside
multiple attributes (['Note','Alias','Parent']).Each row of the
returned array is a arrayref containing the following fields:
column 1 The display name of the feature
column 2 The text of the note
column 3 A relevance score.
column 4 The feature type
column 5 The unique ID of the feature
NOTE: This search will fail to find features that do not have a display name!
You can use fetch() or fetch_many() with the returned IDs to get to
the features themselves.
=cut
sub search_attributes {
my $self = shift;
my ($search_string,$attribute_names,$limit) = @_;
my $attribute_array = ref $attribute_names
&& ref $attribute_names eq 'ARRAY' ? $attribute_names : [$attribute_names];
return $self->_search_attributes($search_string,$attribute_array,$limit);
}
=head2 search_notes
Title : search_notes
Usage : @result_list = $db->search_notes("full text search string",$limit)
Function: Search the notes for a text string
Returns : array of results
Args : full text search string, and an optional feature limit
Status : public
Given a search string, this method performs a full-text search of the
"Notes" attribute and returns an array of results. Each row of the
returned array is a arrayref containing the following fields:
column 1 The display_name of the feature, suitable for passing to get_feature_by_name()
column 2 The text of the note
column 3 A relevance score.
column 4 The type
NOTE: This is equivalent to $db-E<gt>search_attributes('full text search
string','Note',$limit). This search will fail to find features that do
not have a display name!
=cut
###
# search_notes()
#
sub search_notes {
my $self = shift;
my ($search_string,$limit) = @_;
return $self->_search_attributes($search_string,['Note'],$limit);
}
=head2 types
Title : types
Usage : @type_list = $db->types
Function: Get all the types in the database
Returns : array of Bio::DB::GFF::Typename objects
Args : none
Status : public
=cut
sub types {
shift->throw_not_implemented;
}
=head2 insert_sequence
Title : insert_sequence
Usage : $success = $db->insert_sequence($seqid,$sequence_string,$offset)
Function: Inserts sequence data into the database at the indicated offset
Returns : true if successful
Args : see below
Status : public
This method inserts the DNA or protein sequence fragment
$sequence_string, identified by the ID $seq_id, into the database at
the indicated offset $offset. It is used internally by the GFF3Loader
to load sequence data from the files.
=cut
###
# insert_sequence()
#
# insert a bit of primary sequence into the database
#
sub insert_sequence {
my $self = shift;
my ($seqid,$seq,$offset) = @_;
$offset ||= 0;
$self->_insert_sequence($seqid,$seq,$offset);
}
=head2 fetch_sequence
Title : fetch_sequence
Usage : $sequence = $db->fetch_sequence(-seq_id=>$seqid,-start=>$start,-end=>$end)
Function: Fetch the indicated subsequene from the database
Returns : The sequence string (not a Bio::PrimarySeq object!)
Args : see below
Status : public
This method retrieves a portion of the indicated sequence. The arguments are:
Argument Value
-------- -----
-seq_id Chromosome, contig or other DNA segment
-seqid Synonym for -seq_id
-name Synonym for -seq_id
-start Start of range
-end End of range
-class Obsolete argument used for Bio::DB::GFF compatibility. If
specified will qualify the seq_id as "$class:$seq_id".
-bioseq Boolean flag; if true, returns a Bio::PrimarySeq object instead
of a sequence string.
You can call fetch_sequence using the following shortcuts:
$seq = $db->fetch_sequence('chr3'); # entire chromosome
$seq = $db->fetch_sequence('chr3',1000); # position 1000 to end of chromosome
$seq = $db->fetch_sequence('chr3',undef,5000); # position 1 to 5000
$seq = $db->fetch_sequence('chr3',1000,5000); # positions 1000 to 5000
=cut
###
# fetch_sequence()
#
# equivalent to old Bio::DB::GFF->dna() method
#
sub fetch_sequence {
my $self = shift;
my ($seqid,$start,$end,$class,$bioseq) = rearrange([['NAME','SEQID','SEQ_ID'],
'START',['END','STOP'],'CLASS','BIOSEQ'],@_);
$seqid = "$seqid:$class" if defined $class;
my $seq = $self->seq($seqid,$start,$end);
return $seq unless $bioseq;
require Bio::Seq unless Bio::Seq->can('new');
my $display_id = defined $start ? "$seqid:$start..$end" : $seqid;
return Bio::Seq->new(-display_id=>$display_id,-seq=>$seq);
}
=head2 segment
Title : segment
Usage : $segment = $db->segment($seq_id [,$start] [,$end] [,$absolute])
Function: restrict the database to a sequence range
Returns : a Bio::DB::SeqFeature::Segment object
Args : sequence id, start and end ranges (optional)
Status : public
This is a convenience method that can be used when you are interested
in the contents of a particular sequence landmark, such as a
contig. Specify the ID of a sequence or other landmark in the database
and optionally a start and endpoint relative to that landmark. The
method will look up the region and return a
Bio::DB::SeqFeature::Segment object that spans it. You can then use
this segment object to make location-restricted queries on the database.
Example:
$segment = $db->segment('contig23',1,1000); # first 1000 bp of contig23
my @mRNAs = $segment->features('mRNA'); # all mRNAs that overlap segment
Although you will usually want to fetch segments that correspond to
physical sequences in the database, you can actually use any feature
in the database as the sequence ID. The segment() method will perform
a get_features_by_name() internally and then transform the feature
into the appropriate coordinates.
The named feature should exist once and only once in the database. If
it exists multiple times in the database and you attempt to call
segment() in a scalar context, you will get an exception. A workaround
is to call the method in a list context, as in:
my ($segment) = $db->segment('contig23',1,1000);
or
my @segments = $db->segment('contig23',1,1000);
However, having multiple same-named features in the database is often
an indication of underlying data problems.
If the optional $absolute argument is a true value, then the specified
coordinates are relative to the reference (absolute) coordinates.
=cut
###
# Replacement for Bio::DB::GFF->segment() method
#
sub segment {
my $self = shift;
my (@features,@args);
if (@_ == 1 && blessed($_[0])) {
@features = @_;
@args = ();
}
else {
@args = $self->setup_segment_args(@_);
@features = $self->get_features_by_name(@args);
}
if (!wantarray && @features > 1) {
$self->throw(<<END);
segment() called in a scalar context but multiple features match.
Either call in a list context or narrow your search using the -types or -class arguments
END
}
my ($rel_start,$rel_end,$abs) = rearrange(['START',['STOP','END'],'ABSOLUTE'],@args);
$rel_start = 1 unless defined $rel_start;
my @segments;
for my $f (@features) {
my $seqid = $f->seq_id;
my $strand = $f->strand;
my ($start,$end);
if ($abs) {
$start = $rel_start;
$end = defined $rel_end ? $rel_end : $start + $f->length - 1;
}
else {
my $re = defined $rel_end ? $rel_end : $f->end - $f->start + 1;
if ($strand >= 0) {
$start = $f->start + $rel_start - 1;
$end = $f->start + $re - 1;
}
else {
$start = $f->end - $re + 1;
$end = $f->end - $rel_start + 1;
}
}
my $id = eval{$f->primary_id};
push @segments,Bio::DB::SeqFeature::Segment->new($self,$seqid,$start,$end,$strand,$id);
}
return wantarray ? @segments : $segments[0];
}
=head2 seqfeature_class
Title : seqfeature_class
Usage : $classname = $db->seqfeature_class([$new_classname])
Function: get or set the name of the Bio::SeqFeatureI class generated by new_feature()
Returns : name of class
Args : new classname (optional)
Status : public
=cut
sub seqfeature_class {
my $self = shift;
my $d = $self->{seqfeatureclass};
if (@_) {
my $class = shift;
eval "require $class";
$self->throw("$class does not implement the Bio::SeqFeatureI interface")
unless $class->isa('Bio::SeqFeatureI');
$self->{seqfeatureclass} = $class;
}
$d;
}
=head2 reindex
Title : reindex
Usage : $db->reindex
Function: reindex the database
Returns : nothing
Args : nothing
Status : public
This method will force the secondary indexes (name, location,
attributes, feature types) to be recalculated. It may be useful to
rebuild a corrupted database.
=cut
###
# force reindexing
#
sub reindex {
my $self = shift;
my $count = 0;
my $now;
my $last_time = time();
$self->_start_reindexing;
my $iterator = $self->get_seq_stream;
while (my $f = $iterator->next_seq) {
if (++$count %1000 == 0) {
$now = time();
my $elapsed = sprintf(" in %5.2fs",$now - $last_time);
$last_time = $now;
print STDERR "$count features indexed$elapsed...",' 'x60;
print STDERR -t STDOUT && !$ENV{EMACS} ? "\r" : "\n";
}
$self->_update_indexes($f);
}
$self->_end_reindexing;
}
=head2 attributes
Title : attributes
Usage : @a = $db->attributes
Function: Returns list of all known attributes
Returns : Returns list of all known attributes
Args : nothing
Status : public
=cut
sub attributes {
my $self = shift;
shift->throw_not_implemented;
}
=head2 start_bulk_update,finish_bulk_update
Title : start_bulk_update,finish_bulk_update
Usage : $db->start_bulk_update
$db->finish_bulk_update
Function: Activate optimizations for large number of insertions/updates
Returns : nothing
Args : nothing
Status : public
With some adaptors (currently only the DBI::mysql adaptor), these
methods signal the adaptor that a large number of insertions or
updates are to be performed, and activate certain optimizations. These
methods are called automatically by the
Bio::DB::SeqFeature::Store::GFF3Loader module.
Example:
$db->start_bulk_update;
for my $f (@features) {
$db->store($f);
}
$db->finish_bulk_update;
=cut
sub start_bulk_update { shift->_start_bulk_update(@_) }
sub finish_bulk_update { shift->_finish_bulk_update(@_) }
=head2 add_SeqFeature
Title : add_SeqFeature
Usage : $count = $db->add_SeqFeature($parent,@children)
Function: store a parent/child relationship between a $parent and @children
features that are already stored in the database
Returns : number of children successfully stored
Args : parent feature or primary ID and children features or primary IDs
Status : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS
If can_store_parentage() returns true, then some store-aware features
(e.g. Bio::DB::SeqFeature) will invoke this method to store
feature/subfeature relationships in a normalized table.
=cut
# these two are called only if _can_store_subFeatures() returns true
# _add_SeqFeature ($parent,@children)
sub add_SeqFeature { shift->_add_SeqFeature(@_) }
=head2 fetch_SeqFeatures
Title : fetch_SeqFeatures
Usage : @children = $db->fetch_SeqFeatures($parent_feature)
Function: return the immediate subfeatures of the indicated feature
Returns : list of subfeatures
Args : the parent feature and an optional list of children types
Status : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS
If can_store_parentage() returns true, then some store-aware features
(e.g. Bio::DB::SeqFeature) will invoke this method to retrieve
feature/subfeature relationships from the database.
=cut
# _get_SeqFeatures($parent,@child_types)
sub fetch_SeqFeatures {
my ($self, $parent, @child_types) = @_;
return unless defined $parent->primary_id;
$self->_fetch_SeqFeatures($parent,@child_types);
}
=head1 Changing the Behavior of the Database
These methods allow you to modify the behavior of the database.
=head2 debug
Title : debug
Usage : $debug_flag = $db->debug([$new_flag])
Function: set the debug flag
Returns : current debug flag
Args : new debug flag
Status : public
This method gets/sets a flag that turns on verbose progress
messages. Currently this will not do very much.
=cut
sub debug {
my $self = shift;
my $d = $self->{debug};
$self->{debug} = shift if @_;
$d;
}
=head2 serializer
Title : serializer
Usage : $serializer = $db->serializer([$new_serializer])
Function: get/set the name of the serializer
Returns : the name of the current serializer class
Args : (optional) the name of a new serializer
Status : public
You can use this method to set the serializer, but do not attempt to
change the serializer once the database is initialized and populated.
=cut
###
# serializer
#
sub serializer {
my $self = shift;
my $d = $self->setting('serializer');
if (@_) {
my $serializer = shift;
eval "require $serializer; 1" or croak $@;
$self->setting(serializer=>$serializer);
if ($serializer eq 'Storable') {
$Storable::forgive_me =1;
$Storable::Deparse = 1;
$Storable::Eval = 1;
}
}
$d;
}
=head2 dna_accessor
Title : dna_accessor
Usage : $dna_accessor = $db->dna_accessor([$new_dna_accessor])
Function: get/set the name of the dna_accessor
Returns : the current dna_accessor object, if any
Args : (optional) the dna_accessor object
Status : public
You can use this method to request or set the DNA accessor.
=cut
###
# dna_accessor
#
sub dna_accessor {
my $self = shift;
my $d = $self->{dna_accessor};
$self->{dna_accessor} = shift if @_;
$d;
}
sub can_do_seq {
my $self = shift;
my $obj = shift;
return
UNIVERSAL::can($obj,'seq') ||
UNIVERSAL::can($obj,'fetch_sequence');
}
sub set_dna_accessor {
my $self = shift;
my $accessor = shift;
if (-e $accessor) { # a file, assume it is a fasta file
eval "require Bio::DB::Fasta" unless Bio::DB::Fasta->can('new');
my $a = Bio::DB::Fasta->new($accessor)
or croak "Can't open FASTA file $accessor: $!";
$self->dna_accessor($a);
}
if (ref $accessor && $self->can_do_seq($accessor)) {
$self->dna_accessor($accessor); # already built
}
return;
}
sub do_compress {
my $self = shift;
if (@_) {
my $do_compress = shift;
$self->setting(compress => $do_compress);
}
my $d = $self->setting('compress');
if ($d) {
eval "use Compress::Zlib; 1" or croak $@ unless Compress::Zlib->can('compress');
}
$d;
}
=head2 index_subfeatures
Title : index_subfeatures
Usage : $flag = $db->index_subfeatures([$new_value])
Function: flag whether to index subfeatures
Returns : current value of the flag
Args : (optional) new value of the flag
Status : public
If true, the store() method will add a searchable index to both the
top-level feature and all its subfeatures, allowing the search
functions to return features at any level of the containment
hierarchy. If false, only the top level feature will be indexed,
meaning that you will only be able to get at subfeatures by fetching
the top-level feature and then traversing downward using
get_SeqFeatures().
You are free to change this setting at any point during the creation
and population of a database. One database can contain both indexed
and unindexed subfeatures.
=cut
###
# whether to index subfeatures by default
#
sub index_subfeatures {
my $self = shift;
my $d = $self->setting('index_subfeatures');
$self->setting('index_subfeatures'=>shift) if @_;
$d;
}
=head2 clone
The clone() method should be used when you want to pass the
Bio::DB::SeqFeature::Store object to a child process across a
fork(). The child must call clone() before making any queries.
The default behavior is to do nothing, but adaptors that use the DBI
interface may need to implement this in order to avoid database handle
errors. See the dbi adaptor for an example.
=cut
sub clone { }
################################# TIE interface ####################
=head1 TIE Interface
This module implements a full TIEHASH interface. The keys are the
primary IDs of the features in the database. Example:
tie %h,'Bio::DB::SeqFeature::Store',-adaptor=>'DBI::mysql',-dsn=>'dbi:mysql:elegans';
$h{123} = $feature1;
$h{124} = $feature2;
print $h{123}->display_name;
=cut
sub TIEHASH {
my $class = shift;
return $class->new(@_);
}
sub STORE {
my $self = shift;
my ($key,$feature) = @_;
$key =~ /^\d+$/ && $key > 0 or croak "keys must be positive integers";
$self->load_class($feature);
$feature->primary_id($key);
$self->store($feature);
}
sub FETCH {
my $self = shift;
$self->fetch(@_);
}
sub FIRSTKEY {
my $self = shift;
$self->_firstid;
}
sub NEXTKEY {
my $self = shift;
my $lastkey = shift;
$self->_nextid($lastkey);
}
sub EXISTS {
my $self = shift;
my $key = shift;
$self->existsid($key);
}
sub DELETE {
my $self = shift;
my $key = shift;
$self->_deleteid($key);
}
sub CLEAR {
my $self = shift;
$self->_clearall;
}
sub SCALAR {
my $self = shift;
$self->_featurecount;
}
###################### TO BE IMPLEMENTED BY ADAPTOR ##########
=head2 _init_database
Title : _init_database
Usage : $success = $db->_init_database([$erase])
Function: initialize an empty database
Returns : true on success
Args : optional boolean flag to erase contents of an existing database
Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR
This method is the back end for init_database(). It must be
implemented by an adaptor that inherits from
Bio::DB::SeqFeature::Store. It returns true on success. @features = $db->features(-seqid=>'Chr1');
=cut
sub _init_database { shift->throw_not_implemented }
=head2 _store
Title : _store
Usage : $success = $db->_store($indexed,@objects)
Function: store seqfeature objects into database
Returns : true on success
Args : a boolean flag indicating whether objects are to be indexed,
and one or more objects
Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR
This method is the back end for store() and store_noindex(). It should
write the seqfeature objects into the database. If indexing is
requested, the features should be indexed for query and
retrieval. Otherwise the features should be stored without indexing
(it is not required that adaptors respect this).
If the object has no primary_id (undef), then the object is written
into the database and assigned a new primary_id. If the object already
has a primary_id, then the system will perform an update, replacing
whatever was there before.
In practice, the implementation will serialize each object using the
freeze() method and then store it in the database under the
corresponding primary_id. The object is then updated with the
primary_id.
=cut
# _store($indexed,@objs)
sub _store {
my $self = shift;
my $indexed = shift;
my @objs = @_;
$self->throw_not_implemented;
}
=head2 _fetch
Title : _fetch
Usage : $feature = $db->_fetch($primary_id)
Function: fetch feature from database
Returns : feature
Args : primary id
Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR
This method is the back end for fetch(). It accepts a primary_id and
returns a feature object. It must be implemented by the adaptor.
In practice, the implementation will retrieve the serialized
Bio::SeqfeatureI object from the database and pass it to the thaw()
method to unserialize it and synchronize the primary_id.
=cut
# _fetch($id)
sub _fetch { shift->throw_not_implemented }
=head2 _fetch_many
Title : _fetch_many
Usage : $feature = $db->_fetch_many(@primary_ids)
Function: fetch many features from database
Returns : feature
Args : primary id
Status : private -- does not need to be implemented
This method fetches many features specified by a list of IDs. The
default implementation simply calls _fetch() once for each
primary_id. Implementors can override it if needed for efficiency.
=cut
# _fetch_many(@ids)
# this one will fall back to many calls on fetch() if you don't
# override it
sub _fetch_many {
my $self = shift;
return map {$self->_fetch($_)} @_;
}
=head2 _update_indexes
Title : _update_indexes
Usage : $success = $db->_update_indexes($feature)
Function: update the indexes for a feature
Returns : true on success
Args : A seqfeature object
Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY AN ADAPTOR
This method is called by reindex() to update the searchable indexes
for a feature object that has changed.
=cut
# this is called to index a feature
sub _update_indexes { shift->throw_not_implemented }
=head2 _start_reindexing, _end_reindexing
Title : _start_reindexing, _end_reindexing
Usage : $db->_start_reindexing()
$db->_end_reindexing
Function: flag that a series of reindexing operations is beginning/ending
Returns : true on success
Args : none
Status : MAY BE IMPLEMENTED BY AN ADAPTOR (optional)
These methods are called by reindex() before and immediately after a
series of reindexing operations. The default behavior is to do
nothing, but these methods can be overridden by an adaptor in order to
perform optimizations, turn off autocommits, etc.
=cut
# these do not necessary have to be overridden
# they are called at beginning and end of reindexing process
sub _start_reindexing {}
sub _end_reindexing {}
=head2 _features
Title : _features
Usage : @features = $db->_features(@args)
Function: back end for all get_feature_by_*() queries
Returns : list of features
Args : see below
Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR
This is the backend for features(), get_features_by_name(),
get_features_by_location(), etc. Arguments are as described for the
features() method, except that only the named-argument form is
recognized.
=cut
# bottleneck query generator
sub _features { shift->throw_not_implemented }
=head2 _search_attributes
Title : _search_attributes
Usage : @result_list = $db->_search_attributes("text search string",[$tag1,$tag2...],$limit)
Function: back end for the search_attributes() method
Returns : results list
Args : as per search_attributes()
Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR
See search_attributes() for the format of the results list. The only
difference between this and the public method is that the tag list is
guaranteed to be an array reference.
=cut
sub _search_attributes { shift->throw_not_implemented }
=head2 can_store_parentage
Title : can_store_parentage
Usage : $flag = $db->can_store_parentage
Function: return true if this adaptor can store parent/child relationships
Returns : boolean
Args : none
Status : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS
Override this method and return true if this adaptor supports the
_add_SeqFeature() and _get_SeqFeatures() methods, which are used for
storing feature parent/child relationships in a normalized
fashion. Default is false (parent/child relationships are stored in
denormalized form in each feature).
=cut
# return true here if the storage engine is prepared to store parent/child
# relationships using _add_SeqFeature and return them using _fetch_SeqFeatures
sub can_store_parentage { return; }
=head2 _add_SeqFeature
Title : _add_SeqFeature
Usage : $count = $db->_add_SeqFeature($parent,@children)
Function: store a parent/child relationship between $parent and @children
Returns : number of children successfully stored
Args : parent feature and one or more children
Status : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS
If can_store_parentage() returns true, then some store-aware features
(e.g. Bio::DB::SeqFeature) will invoke this method to store
feature/subfeature relationships in a normalized table.
=cut
sub _add_SeqFeature { shift->throw_not_implemented }
=head2 _fetch_SeqFeatures
Title : _fetch_SeqFeatures
Usage : @children = $db->_fetch_SeqFeatures($parent_feature)
Function: return the immediate subfeatures of the indicated feature
Returns : list of subfeatures
Args : the parent feature
Status : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTORS
If can_store_parentage() returns true, then some store-aware features
(e.g. Bio::DB::SeqFeature) will invoke this method to retrieve
feature/subfeature relationships from the database.
=cut
# _get_SeqFeatures($parent,@list_of_child_types)
sub _fetch_SeqFeatures {shift->throw_not_implemented }
=head2 _insert_sequence
Title : _insert_sequence
Usage : $success = $db->_insert_sequence($seqid,$sequence_string,$offset)
Function: Inserts sequence data into the database at the indicated offset
Returns : true if successful
Args : see below
Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR
This is the back end for insert_sequence(). Adaptors must implement
this method in order to store and retrieve nucleotide or protein
sequence.
=cut
sub _insert_sequence { shift->throw_not_implemented }
# _fetch_sequence() is similar to old dna() method
=head2 _fetch_sequence
Title : _fetch_sequence
Usage : $sequence = $db->_fetch_sequence(-seq_id=>$seqid,-start=>$start,-end=>$end)
Function: Fetch the indicated subsequence from the database
Returns : The sequence string (not a Bio::PrimarySeq object!)
Args : see below
Status : ABSTRACT METHOD; MUST BE IMPLEMENTED BY ADAPTOR
This is the back end for fetch_sequence(). Adaptors must implement
this method in order to store and retrieve nucleotide or protein
sequence.
=cut
sub _fetch_sequence { shift->throw_not_implemented }
sub seq {
my $self = shift;
my ($seq_id,$start,$end) = @_;
if (my $a = $self->dna_accessor) {
return $a->can('seq') ? $a->seq($seq_id,$start,$end)
:$a->can('fetch_sequence')? $a->fetch_sequence($seq_id,$start,$end)
: undef;
}
else {
return $self->_fetch_sequence($seq_id,$start,$end);
}
}
=head2 _seq_ids
Title : _seq_ids
Usage : @ids = $db->_seq_ids()
Function: Return all sequence IDs contained in database
Returns : list of sequence Ids
Args : none
Status : TO BE IMPLEMENTED BY ADAPTOR
This method is invoked by seq_ids() to return all sequence IDs
(coordinate systems) known to the database.
=cut
sub _seq_ids { shift->throw_not_implemented }
=head2 _start_bulk_update,_finish_bulk_update
Title : _start_bulk_update, _finish_bulk_update
Usage : $db->_start_bulk_update
$db->_finish_bulk_update
Function: Activate optimizations for large number of insertions/updates
Returns : nothing
Args : nothing
Status : OPTIONAL; MAY BE IMPLEMENTED BY ADAPTOR
These are the backends for start_bulk_update() and
finish_bulk_update(). The default behavior of both methods is to do
nothing.
=cut
# Optional flags to change behavior to optimize bulk updating.
sub _start_bulk_update { }
sub _finish_bulk_update { }
# for full TIE() interface - not necessary to implement in most cases
=head2 Optional methods needed to implement full TIEHASH interface
The core TIEHASH interface will work if just the _store() and _fetch()
methods are implemented. To support the full TIEHASH interface,
including support for keys(), each(), and exists(), the following
methods should be implemented:
=over 4
=item $id = $db-E<gt>_firstid()
Return the first primary ID in the database. Needed for the each()
function.
=item $next_id = $db-E<gt>_nextid($id)
Given a primary ID, return the next primary ID in the series. Needed
for the each() function.
=item $boolean = $db-E<gt>_existsid($id)
Returns true if the indicated primary ID is in the database. Needed
for the exists() function.
=item $db-E<gt>_deleteid($id)
Delete the feature corresponding to the given primary ID. Needed for
delete().
=item $db-E<gt>_clearall()
Empty the database. Needed for %tied_hash = ().
=item $count = $db-E<gt>_featurecount()
Return the number of features in the database. Needed for scalar
%tied_hash.
=back
=cut
sub _firstid { shift->throw_not_implemented }
sub _nextid { shift->throw_not_implemented }
sub _existsid { shift->throw_not_implemented }
sub _deleteid { shift->throw_not_implemented }
sub _clearall { shift->throw_not_implemented }
sub _featurecount { shift->throw_not_implemented }
=head1 Internal Methods
These methods are internal to Bio::DB::SeqFeature::Store and adaptors.
=head2 new_instance
Title : new_instance
Usage : $db = $db->new_instance()
Function: class constructor
Returns : A descendent of Bio::DB::SeqFeature::Store
Args : none
Status : internal
This method is called internally by new() to create a new
uninitialized instance of Bio::DB::SeqFeature::Store. It is used
internally and should not be called by application software.
=cut
sub new_instance {
my $class = shift;
return bless {},ref($class) || $class;
}
=head2 init
Title : init
Usage : $db->init(@args)
Function: initialize object
Returns : none
Args : Arguments passed to new()
Status : private
This method is called internally by new() to initialize a
newly-created object using the arguments passed to new(). It is to be
overridden by Bio::DB::SeqFeature::Store adaptors.
=cut
sub init {
my $self = shift;
$self->default_settings();
}
=head2 default_settings
Title : default_settings
Usage : $db->default_settings()
Function: set up default settings for the adaptor
Returns : none
Args : none
Status : private
This method is may be overridden by adaptors. It is responsible for
setting up object default settings.
=cut
###
# default settings -- set up whatever are the proper default settings
#
sub default_settings {
my $self = shift;
$self->serializer($self->default_serializer);
$self->index_subfeatures(1);
}
=head2 default_serializer
Title : default_serializer
Usage : $serializer = $db->default_serializer
Function: finds an available serializer
Returns : the name of an available serializer
Args : none
Status : private
This method returns the name of an available serializer module.
=cut
###
# choose a serializer
#
sub default_serializer {
my $self = shift;
# try Storable
eval "require Storable; 1" and return 'Storable';
eval "require Data::Dumper; 1" and return 'Data::Dumper';
croak "Unable to load either Storable or Data::Dumper. Please provide a serializer using -serializer";
}
=head2 setting
Title : setting
Usage : $value = $db->setting('setting_name' [=> $new_value])
Function: get/set the value of a setting
Returns : the value of the current setting
Args : the name of the setting and optionally a new value for the setting
Status : private
This is a low-level procedure for persistently storing database
settings. It can be overridden by adaptors.
=cut
# persistent settings
# by default we store in the object
sub setting {
my $self = shift;
my $variable_name = shift;
my $d = $self->{setting}{$variable_name};
$self->{setting}{$variable_name} = shift if @_;
$d;
}
=head2 subfeatures_are_indexed
Title : subfeatures_are_indexed
Usage : $flag = $db->subfeatures_are_indexed([$new_value])
Function: flag whether subfeatures are indexed
Returns : a flag indicating that all subfeatures are indexed
Args : (optional) new value of the flag
Status : private
This method is used internally by the Bio::DB::SeqFeature class to
optimize some of its operations. It returns true if all of the
subfeatures in the database are indexed; it returns false if at least
one of the subfeatures is not indexed. Do not attempt to change the
value of this setting unless you are writing an adaptor.
=cut
###
# whether subfeatures are all indexed
#
sub subfeatures_are_indexed {
my $self = shift;
my $d = $self->setting('subfeatures_are_indexed');
$self->setting(subfeatures_are_indexed => shift) if @_;
$d;
}
=head2 subfeature_types_are_indexed
Title : subfeature_types_are_indexed
Usage : $flag = $db->subfeature_types_are_indexed
Function: whether subfeatures are indexed by type
Returns : a flag indicating that all subfeatures are indexed
Args : none
Status : private
This method returns true if subfeature types are indexed. Default is
to return the value of subfeatures_are_indexed().
=cut
sub subfeature_types_are_indexed {
my $self = shift;
return $self->subfeatures_are_indexed;
}
=head2 subfeature_locations_are_indexed
Title : subfeature_locations_are_indexed
Usage : $flag = $db->subfeature_locations_are_indexed
Function: whether subfeatures are indexed by type
Returns : a flag indicating that all subfeatures are indexed
Args : none
Status : private
This method returns true if subfeature locations are indexed. Default is
to return the value of subfeatures_are_indexed().
=cut
sub subfeature_locations_are_indexed {
my $self = shift;
return $self->subfeatures_are_indexed;
}
=head2 setup_segment_args
Title : setup_segment_args
Usage : @args = $db->setup_segment_args(@args)
Function: munge the arguments to the segment() call
Returns : munged arguments
Args : see below
Status : private
This method is used internally by segment() to translate positional
arguments into named argument=E<gt>value pairs.
=cut
sub setup_segment_args {
my $self = shift;
return @_ if defined $_[0] && $_[0] =~ /^-/;
return (-name=>$_[0],-start=>$_[1],-end=>$_[2]) if @_ == 3;
return (-class=>$_[0],-name=>$_[1]) if @_ == 2;
return (-name=>$_[0]) if @_ == 1;
return;
}
=head2 store_and_cache
Title : store_and_cache
Usage : $success = $db->store_and_cache(@features)
Function: store features into database and update cache
Returns : number of features stored
Args : index the features? (0 or 1) and list of features
Status : private
This private method stores the list of Bio::SeqFeatureI objects into
the database and caches them in memory for retrieval.
=cut
sub store_and_cache {
my $self = shift;
my $indexit = shift;
my $result = $self->_store($indexit,@_);
if (my $cache = $self->cache) {
for my $obj (@_) {
defined (my $id = eval {$obj->primary_id}) or next;
$cache->store($id,$obj);
}
}
$result;
}
=head2 init_cache
Title : init_cache
Usage : $db->init_cache($size)
Function: initialize the in-memory feature cache
Returns : the Tie::Cacher object
Args : desired size of the cache
Status : private
This method is used internally by new() to create the Tie::Cacher
instance used for the in-memory feature cache.
=cut
sub init_cache {
my $self = shift;
my $cache_size = shift;
$cache_size = 5000 if $cache_size == 1; # in case somebody treats it as a flag
$self->{cache} = Tie::Cacher->new($cache_size) or $self->throw("Couldn't tie cache: $!");
}
=head2 cache
Title : cache
Usage : $cache = $db->cache
Function: return the cache object
Returns : the Tie::Cacher object
Args : none
Status : private
This method returns the Tie::Cacher object used for the in-memory
feature cache.
=cut
sub cache { shift->{cache} }
=head2 load_class
Title : load_class
Usage : $db->load_class($blessed_object)
Function: loads the module corresponding to a blessed object
Returns : empty
Args : a blessed object
Status : private
This method is used by thaw() to load the code for a blessed
object. This ensures that all the object's methods are available.
=cut
sub load_class {
my $self = shift;
my $obj = shift;
return unless defined $obj;
return if $self->{class_loaded}{ref $obj}++;
unless ($obj && $obj->can('primary_id')) {
my $class = ref $obj;
eval "require $class";
}
}
#################################### Internal methods ####################
=head2 freeze
Title : freeze
Usage : $serialized_object = $db->freeze($feature)
Function: serialize a feature object into a string
Returns : serialized feature object
Args : a seqfeature object
Status : private
This method converts a Bio::SeqFeatureI object into a serialized form
suitable for storage into a database. The feature's primary ID is set
to undef before it is serialized. This avoids any potential mismatch
between the primary ID used as the database key and the primary ID
stored in the serialized object.
=cut
sub freeze {
my $self = shift;
my $obj = shift;
# Bio::SeqFeature::Generic contains cleanup methods, so we need to
# localize the methods to undef temporarily so that we can serialize
local $obj->{'_root_cleanup_methods'} if exists $obj->{'_root_cleanup_methods'};
my ($id,$store);
$id = $obj->primary_id();
$obj->primary_id(undef); # don't want primary ID to be stored in object
eval {
$store = $obj->object_store;
$obj->object_store(undef); # don't want a copy of the store in the object
};
my $serializer = $self->serializer;
my $data;
if ($serializer eq 'Data::Dumper') {
my $d = Data::Dumper->new([$obj]);
$d->Terse(1);
$d->Deepcopy(1);
$data = $d->Dump;
} elsif ($serializer eq 'Storable') {
$data = Storable::nfreeze($obj);
}
$obj->primary_id($id); # restore to original state
eval {
$obj->object_store($store);
};
$data = compress($data) if $self->do_compress;
return $data;
}
=head2 thaw
Title : thaw
Usage : $feature = $db->thaw($serialized_object,$primary_id)
Function: unserialize a string into a feature object
Returns : Bio::SeqFeatureI object
Args : serialized form of object from freeze() and primary_id of object
Status : private
This method is the reverse of the freeze(). The supplied primary_id
becomes the primary_id() of the returned Bio::SeqFeatureI object. This
implementation checks for a deserialized object in the cache before it
calls thaw_object() to do the actual deserialization.
=cut
sub thaw {
my $self = shift;
my ($obj,$primary_id) = @_;
if (my $cache = $self->cache) {
return $cache->fetch($primary_id) if $cache->exists($primary_id);
my $object = $self->thaw_object($obj,$primary_id) or return;
$cache->store($primary_id,$object);
return $object;
} else {
return $self->thaw_object($obj,$primary_id);
}
}
=head2 thaw_object
Title : thaw_object
Usage : $feature = $db->thaw_object($serialized_object,$primary_id)
Function: unserialize a string into a feature object
Returns : Bio::SeqFeatureI object
Args : serialized form of object from freeze() and primary_id of object
Status : private
After thaw() checks the cache and comes up empty, this method is
invoked to thaw the object.
=cut
sub thaw_object {
my $self = shift;
my ($obj,$primary_id) = @_;
my $serializer = $self->serializer;
my $object;
$obj = uncompress($obj) if $self->do_compress;
if ($serializer eq 'Data::Dumper') {
$object = eval $obj;
} elsif ($serializer eq 'Storable') {
$object = Storable::thaw($obj);
}
# remember the primary ID of this object as well as the
# identity of the store, so that we can do lazy loading;
# both of these are wrapped in an eval because not all
# bioseqfeatures support them (or want to)
$self->load_class($object);
eval {
$object->primary_id($primary_id);
$object->object_store($self);
};
$object;
}
=head2 feature_names
Title : feature_names
Usage : ($names,$aliases) = $db->feature_names($feature)
Function: get names and aliases for a feature
Returns : an array of names and an array of aliases
Args : a Bio::SeqFeatureI object
Status : private
This is an internal utility function which, given a Bio::SeqFeatureI
object, returns two array refs. The first is a list of official names
for the feature, and the second is a list of aliases. This is slightly
skewed towards GFF3 usage, so the official names are the
display_name(), plus all tag values named 'Name', plus all tag values
named 'ID'. The aliases are all tag values named 'Alias'.
=cut
sub feature_names {
my $self = shift;
my $obj = shift;
my $primary_id = $obj->primary_id;
my @names;
push @names,$obj->display_name if defined $obj->display_name;
push @names,$obj->get_tag_values('Name') if $obj->has_tag('Name');
push @names,$obj->get_tag_values('ID') if $obj->has_tag('ID');
# don't think this is desired behavior
# @names = grep {defined $_ && $_ ne $primary_id} @names;
my @aliases = grep {defined} $obj->get_tag_values('Alias') if $obj->has_tag('Alias');
return (\@names,\@aliases);
}
=head2 feature_summary
Title : feature_summary
Usage : $summary = $db->feature_summary(@args)
Function: returns a coverage summary across indicated region/type
Returns : a Bio::SeqFeatureI object containing the "coverage" tag
Args : see below
Status : public
This method is used to get coverage density information across a
region of interest. You provide it with a region of interest, optional
a list of feature types, and a count of the number of bins over which
you want to calculate the coverage density. An object is returned
corresponding to the requested region. It contains a tag called
"coverage" that will return an array ref of "bins" length. Each
element of the array describes the number of features that overlap the
bin at this postion.
Arguments:
Argument Description
-------- -----------
-seq_id Sequence ID for the region
-start Start of region
-end End of region
-type/-types Feature type of interest or array ref of types
-bins Number of bins across region. Defaults to 1000.
-iterator Return an iterator across the region
Note that this method uses an approximate algorithm that is only
accurate to 500 bp, so when dealing with bins that are smaller than
1000 bp, you may see some shifting of counts between adjacent bins.
Although an -iterator option is provided, the method only ever returns
a single feature, so this is fairly useless.
=cut
sub feature_summary {
my $self = shift;
my ($seq_name,$start,$end,$types,$bins,$iterator) =
rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'],
['TYPES','TYPE','PRIMARY_TAG'],
'BINS',
'ITERATOR',
],@_);
my ($coverage,$tag) = $self->coverage_array(-seqid=> $seq_name,
-start=> $start,
-end => $end,
-type => $types,
-bins => $bins) or return;
my $score = 0;
for (@$coverage) { $score += $_ }
$score /= @$coverage;
my $feature = Bio::SeqFeature::Lite->new(-seq_id => $seq_name,
-start => $start,
-end => $end,
-type => $tag,
-score => $score,
-attributes =>
{ coverage => [$coverage] });
return $iterator
? Bio::DB::SeqFeature::Store::FeatureIterator->new($feature)
: $feature;
}
=head2 coverage_array
Title : coverage_array
Usage : $arrayref = $db->coverage_array(@args)
Function: returns a coverage summary across indicated region/type
Returns : an array reference
Args : see below
Status : public
This method is used to get coverage density information across a
region of interest. The arguments are identical to feature_summary,
except that instead of returning a Bio::SeqFeatureI object, it returns
an array reference of the desired number of bins. The value of each
element corresponds to the number of features in the bin.
Arguments:
Argument Description
-------- -----------
-seq_id Sequence ID for the region
-start Start of region
-end End of region
-type/-types Feature type of interest or array ref of types
-bins Number of bins across region. Defaults to 1000.
Note that this method uses an approximate algorithm that is only
accurate to 500 bp, so when dealing with bins that are smaller than
1000 bp, you may see some shifting of counts between adjacent bins.
=cut
sub coverage_array {
shift->throw_not_implemented;
}
package Bio::DB::SeqFeature::Store::FeatureIterator;
sub new {
my $self = shift;
my @features = @_;
return bless \@features,ref $self || $self;
}
sub next_seq {
my $self = shift;
return unless @$self;
return shift @$self;
}
sub begin_work { }# noop
sub commit { }# noop
sub rollback { }# noop
1;
__END__
=head1 BUGS
This is an early version, so there are certainly some bugs. Please
use the BioPerl bug tracking system to report bugs.
=head1 SEE ALSO
L<Bio::DB::SeqFeature>,
L<Bio::DB::SeqFeature::Store::GFF3Loader>,
L<Bio::DB::SeqFeature::Segment>,
L<Bio::DB::SeqFeature::Store::DBI::mysql>,
L<Bio::DB::SeqFeature::Store::berkeleydb>
L<Bio::DB::SeqFeature::Store::memory>
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
Copyright (c) 2006 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=cut