Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::DB::SeqFeature::Store::GFF2Loader -- GFF2 file loader for Bio::DB::SeqFeature::Store

SYNOPSIS

         use Bio::DB::SeqFeature::Store;
         use Bio::DB::SeqFeature::Store::GFF2Loader;

         # Open the sequence database
         my $db      = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql',
                                                        -dsn     => 'dbi:mysql:test',
                                                        -write   => 1 );

         my $loader = Bio::DB::SeqFeature::Store::GFF2Loader->new(-store    => $db,
                                                                  -verbose  => 1,
                                                                  -fast     => 1);

         $loader->load('./my_genome.gff');

DESCRIPTION

       The Bio::DB::SeqFeature::Store::GFF2Loader object parsers GFF2-format sequence annotation
       files and loads Bio::DB::SeqFeature::Store databases. For certain combinations of
       SeqFeature classes and SeqFeature::Store databases it features a "fast load" mode which
       will greatly accelerate the loading of GFF2 databases by a factor of 5-10.

       The GFF2 file format has been extended very slightly to accommodate
       Bio::DB::SeqFeature::Store. First, the loader recognizes is a new directive:

         # #index-subfeatures [0|1]

       Note that you can place a space between the two #'s in order to prevent GFF2 validators
       from complaining.

       If this is true, then subfeatures are indexed (the default) so that they can be retrieved
       with a query. See Bio::DB::SeqFeature::Store for an explanation of this. If false, then
       subfeatures can only be accessed through their parent feature. The default is to index all
       subfeatures.

       Second, the loader recognizes a new attribute tag called index, which if present, controls
       indexing of the current feature. Example:

        ctg123 . TF_binding_site 1000 1012 . + . ID=tfbs00001;index=1

       You can use this to turn indexing on and off, overriding the default for a particular
       feature.

   new
        Title   : new
        Usage   : $loader = Bio::DB::SeqFeature::Store::GFF2Loader->new(@options)
        Function: create a new parser
        Returns : a Bio::DB::SeqFeature::Store::GFF2Loader gff2 parser and loader
        Args    : several - see below
        Status  : public

       This method creates a new GFF2 loader and establishes its connection with a
       Bio::DB::SeqFeature::Store database. Arguments are -name=>$value pairs as described in
       this table:

        Name               Value
        ----               -----

        -store             A writable Bio::DB::SeqFeature::Store database handle.

        -seqfeature_class  The name of the type of Bio::SeqFeatureI object to create
                             and store in the database (Bio::DB::SeqFeature by default)

        -sf_class          A shorter alias for -seqfeature_class

        -verbose           Send progress information to standard error.

        -fast              If true, activate fast loading (see below)

        -chunk_size        Set the storage chunk size for nucleotide/protein sequences
                              (default 2000 bytes)

        -tmp               Indicate a temporary directory to use when loading non-normalized
                              features.

       When you call new(), a connection to a Bio::DB::SeqFeature::Store database should already
       have been established and the database initialized (if appropriate).

       Some combinations of Bio::SeqFeatures and Bio::DB::SeqFeature::Store databases support a
       fast loading mode. Currently the only reliable implementation of fast loading is the
       combination of DBI::mysql with Bio::DB::SeqFeature. The other important restriction on
       fast loading is the requirement that a feature that contains subfeatures must occur in the
       GFF2 file before any of its subfeatures. Otherwise the subfeatures that occurred before
       the parent feature will not be attached to the parent correctly. This restriction does not
       apply to normal (slow) loading.

       If you use an unnormalized feature class, such as Bio::SeqFeature::Generic, then the
       loader needs to create a temporary database in which to cache features until all their
       parts and subparts have been seen. This temporary databases uses the "berkeleydb" adaptor.
       The -tmp option specifies the directory in which that database will be created. If not
       present, it defaults to the system default tmp directory specified by
       File::Spec->tmpdir().

       The -chunk_size option allows you to tune the representation of DNA/Protein sequence in
       the Store database. By default, sequences are split into 2000 base/residue chunks and then
       reassembled as needed. This avoids the problem of pulling a whole chromosome into memory
       in order to fetch a short subsequence from somewhere in the middle. Depending on your
       usage patterns, you may wish to tune this parameter using a chunk size that is larger or
       smaller than the default.

   load
        Title   : load
        Usage   : $count = $loader->load(@ARGV)
        Function: load the indicated files or filehandles
        Returns : number of feature lines loaded
        Args    : list of files or filehandles
        Status  : public

       Once the loader is created, invoke its load() method with a list of GFF2 or FASTA file
       paths or previously-opened filehandles in order to load them into the database. Compressed
       files ending with .gz, .Z and .bz2 are automatically recognized and uncompressed on the
       fly. Paths beginning with http: or ftp: are treated as URLs and opened using the LWP GET
       program (which must be on your path).

       FASTA files are recognized by their initial ">" character. Do not feed the loader a file
       that is neither GFF2 nor FASTA; I don't know what will happen, but it will probably not be
       what you expect.

   accessors
       The following read-only accessors return values passed or created during new():

        store()          the long-term Bio::DB::SeqFeature::Store object

        tmp_store()      the temporary Bio::DB::SeqFeature::Store object used
                           during loading

        sfclass()        the Bio::SeqFeatureI class

        fast()           whether fast loading is active

        seq_chunk_size() the sequence chunk size

        verbose()        verbose progress messages

   Internal Methods
       The following methods are used internally and may be overidden by subclasses.

       default_seqfeature_class
             $class = $loader->default_seqfeature_class

           Return the default SeqFeatureI class (Bio::DB::SeqFeature).

       subfeatures_normalized
             $flag = $loader->subfeatures_normalized([$new_flag])

           Get or set a flag that indicates that the subfeatures are normalized. This is deduced
           from the SeqFeature class information.

       subfeatures_in_table
             $flag = $loader->subfeatures_in_table([$new_flag])

           Get or set a flag that indicates that feature/subfeature relationships are stored in a
           table. This is deduced from the SeqFeature class and Store information.

       load_fh
             $count = $loader->load_fh($filehandle)

           Load the GFF2 data at the other end of the filehandle and return true if successful.
           Internally, load_fh() invokes:

             start_load();
             do_load($filehandle);
             finish_load();

       start_load, finish_load
           These methods are called at the start and end of a filehandle load.

       do_load
             $count = $loader->do_load($fh)

           This is called by load_fh() to load the GFF2 file's filehandle and return the number
           of lines loaded.

       load_line
               $loader->load_line($data);

           Load a line of a GFF2 file. You must bracket this with calls to start_load() and
           finish_load()!

               $loader->start_load();
               $loader->load_line($_) while <FH>;
               $loader->finish_load();

       handle_meta
             $loader->handle_meta($meta_directive)

           This method is called to handle meta-directives such as ##sequence-region. The method
           will receive the directive with the initial ## stripped off.

       handle_feature
             $loader->handle_feature($gff2_line)

           This method is called to process a single GFF2 line. It manipulates information stored
           a data structure called $self->{load_data}.

       store_current_feature
             $loader->store_current_feature()

           This method is called to store the currently active feature in the database. It uses a
           data structure stored in $self->{load_data}.

       build_object_tree
            $loader->build_object_tree()

           This method gathers together features and subfeatures and builds the graph that
           connects them.

       build_object_tree_in_tables
            $loader->build_object_tree_in_tables()

           This method gathers together features and subfeatures and builds the graph that
           connects them, assuming that parent/child relationships will be stored in a database
           table.

       build_object_tree_in_features
            $loader->build_object_tree_in_features()

           This method gathers together features and subfeatures and builds the graph that
           connects them, assuming that parent/child relationships are stored in the seqfeature
           objects themselves.

       attach_children
            $loader->attach_children($store,$load_data,$load_id,$feature)

           This recursively adds children to features and their subfeatures. It is called when
           subfeatures are directly contained within other features, rather than stored in a
           relational table.

       fetch
            my $feature = $loader->fetch($load_id)

           Given a load ID (from the ID= attribute) this method returns the feature from the
           temporary database or the permanent one, depending on where it is stored.

       add_segment
            $loader->add_segment($parent,$child)

           This method is used to add a split location to the parent.

       parse_attributes
            ($reserved,$unreserved) = $loader->parse_attributes($attribute_line)

           This method parses the information contained in the $attribute_line into two hashrefs,
           one containing the values of reserved attribute tags (e.g. ID) and the other
           containing the values of unreserved ones.

       start_or_finish_sequence
             $loader->start_or_finish_sequence('Chr9')

           This method is called at the beginning and end of a fasta section.

       load_sequence
             $loader->load_sequence('gatttcccaaa')

           This method is called to load some amount of sequence after start_or_finish_sequence()
           is first called.

       open_fh
            my $io_file = $loader->open_fh($filehandle_or_path)

           This method opens up the indicated file or pipe, using some intelligence to recognized
           compressed files and URLs and doing the right thing.

       time
            my $time = $loader->time

           This method returns the current time in seconds, using Time::HiRes if available.

       unescape
            my $unescaped = GFF2Loader::unescape($escaped)

           This is an internal utility.  It is the same as CGI::Util::unescape, but doesn't
           change pluses into spaces and ignores unicode escapes.

BUGS

       This is an early version, so there are certainly some bugs. Please use the BioPerl bug
       tracking system to report bugs.

SEE ALSO

       bioperl, Bio::DB::SeqFeature::Store, Bio::DB::SeqFeature::Segment,
       Bio::DB::SeqFeature::NormalizedFeature, Bio::DB::SeqFeature::GFF3Loader,
       Bio::DB::SeqFeature::Store::DBI::mysql, Bio::DB::SeqFeature::Store::berkeleydb

AUTHOR

       Lincoln Stein <lstein@cshl.org>.

       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.