NAME

Bio::DB::SeqFeature::Store -- Storage and retrieval of sequence annotation data

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:

No limitation on Bio::SeqFeatureI implementations

Unlike Bio::DB::GFF, Bio::DB::SeqFeature::Store works with any Bio::SeqFeatureI object.
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.
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).
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 link

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=>$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);

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.

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 <lstein@cshl.org>.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

To install Bio::Seq, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Seq

CPAN shell

perl -MCPAN -e shell
install Bio::Seq

For more information on module installation, please visit the detailed CPAN module installation guide.

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