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');
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:- 1.
-
No limitation on Bio::SeqFeatureI implementations
Unlike Bio::DB::GFF, Bio::DB::SeqFeature::Store works with any Bio::SeqFeatureI object.
- 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.
- 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).
- 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.
We'll discuss major concepts in Bio::DB::SeqFeature::Store and then describe how to use the module.
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.- 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).
- DBI::mysql
- A full-featured implementation on top of the MySQL relational database system.
- berkeleydb
- A full-feature implementation that runs on top of the BerkeleyDB database. See Bio::DB::SeqFeature::Store::berkeleydb.
If you do not explicitly specify the adaptor, then DBI::mysql will be used by default.
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- Storable
- This is a fast binary serializer. It is available in Perl versions 5.8.7 and higher and is used when available.
- 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.
If you do not specify the serializer, then Storable will be used if available; otherwise Data::Dumper.
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 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.
Methods for Connecting and Initializating a Database
## TODO: http://iowg.brcdevel.org/gff3.html#a_fasta is a dead linknew
Title : new Usage : $db = Bio::DB::SeqFeature::Store->new(@options) Function: connect to a database Returns : A descendent of Bio::DB::Seqfeature::Store Args : several - see below Status : public
This class method creates a new database connection. The following -name=>$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 -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 -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 -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 -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.
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->new() to initialize a new database. In the case of a DBI database, this method installs the schema but does 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.
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.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
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 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.
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.
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).
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->new(), which in turn are similar to Bio::SeqFeature::Generic->new() and Bio::Graphics::Feature->new(). The most important difference is the -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->seqfeature_class().
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.
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.
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.
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->features().
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().
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.
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.
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 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''.
get_features_by_location
Title : get_features_by_location Usage : @features = $db->get_features_by_location(@args) Function: looks up features by their location Returns : a list of matching features Args : see below Status : public
This method fetches features based on a location range lookup. You call it using a positional list of arguments, or a list of (-argument=>$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 -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 -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.
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);
features
Title : features Usage : @features = $db->features(@args) Function: generalized query & retrieval interface Returns : list of features Args : see below Status : Public
This is the workhorse for feature query and retrieval. It takes a series of -name=>$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 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');
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
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
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.
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 $db->search_attributes('full text search string','Note',$limit). This search will fail to find features that do not have a display name!
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
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.
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
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.
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
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.
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
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;
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.
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.
Changing the Behavior of the Database
These methods allow you to modify the behavior of the database.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.
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.
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.
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.
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.
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;
_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');
_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.
_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.
_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.
_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.
_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.
_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.
_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.
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).
_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.
_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.
_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.
_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.
_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.
_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.
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:- $id = $db->_firstid()
- Return the first primary ID in the database. Needed for the each() function.
- $next_id = $db->_nextid($id)
- Given a primary ID, return the next primary ID in the series. Needed for the each() function.
- $boolean = $db->_existsid($id)
- Returns true if the indicated primary ID is in the database. Needed for the exists() function.
- $db->_deleteid($id)
- Delete the feature corresponding to the given primary ID. Needed for delete().
- $db->_clearall()
- Empty the database. Needed for %tied_hash = ().
- $count = $db->_featurecount()
- Return the number of features in the database. Needed for scalar %tied_hash.
Internal Methods
These methods are internal to Bio::DB::SeqFeature::Store and adaptors.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.
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.
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.
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.
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.
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.
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().
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().
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=>value pairs.
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.
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.
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.
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.
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.
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.
thaw_object
Title : thaw_object Usage : $feature = $db->thaw_object($serialized_object,$primary_id) Function: unserialize a string into a feature object Returns : Bio::SeqFeatureI object Args : serialized form of object from freeze() and primary_id of object Status : private
After thaw() checks the cache and comes up empty, this method is invoked to thaw the object.
feature_names
Title : feature_names Usage : ($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'.
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.
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.
BUGS
This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs.AUTHOR
Lincoln Stein <[email protected]>.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.