Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::DB::SeqFeature::Store::FeatureFileLoader -- feature file loader for
       Bio::DB::SeqFeature::Store

SYNOPSIS

         use Bio::DB::SeqFeature::Store;
         use Bio::DB::SeqFeature::Store::FeatureFileLoader;

         # 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::FeatureFileLoader->new(-store    => $db,
                                                              -verbose  => 1,
                                                              -fast     => 1);

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

DESCRIPTION

       The Bio::DB::SeqFeature::Store::FeatureFileLoader object parsers FeatureFile-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 databases by a factor of 5-10.

       FeatureFile Format (.fff) is very simple:

        mRNA B0511.1 Chr1:1..100 Type=UTR;Note="putative primase"
        mRNA B0511.1 Chr1:101..200,300..400,500..800 Type=CDS
        mRNA B0511.1 Chr1:801..1000 Type=UTR

        reference = Chr3
        Cosmid B0511   516..619
        Cosmid B0511   3185..3294
        Cosmid B0511   10946..11208
        Cosmid B0511   13126..13511
        Cosmid B0511   11394..11539
        EST    yk260e10.5      15569..15724
        EST    yk672a12.5      537..618,3187..3294
        EST    yk595e6.5       552..618
        EST    yk595e6.5       3187..3294
        EST    yk846e07.3      11015..11208
        EST    yk53c10
               yk53c10.3       15000..15500,15700..15800
               yk53c10.5       18892..19154
        EST    yk53c10.5       16032..16105
        SwissProt      PECANEX 13153-13656     Note="Swedish fish"
        FGENESH        "Predicted gene 1"      1-205,518-616,661-735,3187-3365,3436-3846       "Pfam domain"
        # file ends

       There are up to four columns of WHITESPACE (not necessarily tab) delimited text. Embedded
       whitespace must be escaped using shell escaping rules (quoting the column or backslashing
       whitespace).

         Column 1: The feature type. You may use type:subtype as a convention
                   for method:source.

         Column 2: The feature name/ID.

         Column 3: The position of this feature in base pair
                   coordinates. Ranges can be given as either
                   start-end or start..end. A chromosome position
                   can be specified using the format "reference:start..end".
                   A discontinuous feature can be specified by giving
                   multiple ranges separated by commas. Minus-strand features
                   are indicated by specifying a start > end.

         Column 4: Comment/attribute field. A single Note can be given, or
                   a series of attribute=value pairs, separated by
                   spaces or semicolons, as in "score=23;type=transmembrane"

   Specifying Positions and Ranges
       A feature position is specified using a sequence ID (a genbank accession number, a
       chromosome name, a contig, or any other meaningful reference system, followed by a colon
       and a position range. Ranges are two integers separated by double dots or the hyphen.
       Examples: "Chr1:516..11208", "ctgA:1-5000". Negative coordinates are allowed, as in
       "Chr1:-187..1000".

       A discontinuous range ("split location") uses commas to separate the ranges.  For example:

        Gene B0511.1  Chr1:516..619,3185..3294,10946..11208

       In the case of a split location, the sequence id only has to appear in front of the first
       range.

       Alternatively, a split location can be indicated by repeating the features type and name
       on multiple adjacent lines:

        Gene   B0511.1 Chr1:516..619
        Gene   B0511.1 Chr1:3185..3294
        Gene   B0511.1 Chr1:10946..11208

       If all the locations are on the same reference sequence, you can specify a default
       chromosome using a "reference=<seqid>":

        reference=Chr1
        Gene   B0511.1 516..619
        Gene   B0511.1 3185..3294
        Gene   B0511.1 10946..11208

       The default seqid is in effect until the next "reference" line appears.

   Feature Tags
       Tags can be added to features by adding a fourth column consisting of "tag=value" pairs:

        Gene  B0511.1  Chr1:516..619,3185..3294 Note="Putative primase"

       Tags and their values take any form you want, and multiple tags can be separated by
       semicolons. You can also repeat tags multiple times:

        Gene  B0511.1  Chr1:516..619,3185..3294 GO_Term=GO:100;GO_Term=GO:2087

       Several tags have special meanings:

        Tag     Meaning
        ---     -------

        Type    The primary tag for a subfeature.
        Score   The score of a feature or subfeature.
        Phase   The phase of a feature or subfeature.
        URL     A URL to link to (via the Bio::Graphics library).
        Note    A note to attach to the feature for display by the Bio::Graphics library.

       For example, in the common case of an mRNA, you can use the "Type" tag to distinguish the
       parts of the mRNA into UTR and CDS:

        mRNA B0511.1 Chr1:1..100 Type=UTR
        mRNA B0511.1 Chr1:101..200,300..400,500..800 Type=CDS
        mRNA B0511.1 Chr1:801..1000 Type=UTR

       The top level feature's primary tag will be "mRNA", and its subparts will have types UTR
       and CDS as indicated. Additional tags that are placed in the first line of the feature
       will be applied to the top level. In this example, the note "Putative primase" will be
       applied to the mRNA at the top level of the feature:

        mRNA B0511.1 Chr1:1..100 Type=UTR;Note="Putative primase"
        mRNA B0511.1 Chr1:101..200,300..400,500..800 Type=CDS
        mRNA B0511.1 Chr1:801..1000 Type=UTR

   Feature Groups
       Features can be grouped so that they are rendered by the "group" glyph.  To start a group,
       create a two-column feature entry showing the group type and a name for the group.  Follow
       this with a list of feature entries with a blank type.  For example:

        EST    yk53c10
               yk53c10.3       15000-15500,15700-15800
               yk53c10.5       18892-19154

       This example is declaring that the ESTs named yk53c10.3 and yk53c10.5 belong to the same
       group named yk53c10.

   Comments and the #include Directive
       Lines that begin with the # sign are treated as comments and ignored. When a # sign
       appears within a line, everything to the right of the symbol is also ignored, unless it
       looks like an HTML fragment or an HTML color, e.g.:

        # this is ignored
        [Example]
        glyph   = generic   # this comment is ignored
        bgcolor = #FF0000
        link    = http://www.google.com/search?q=$name#results

       Be careful, because the processing of # signs uses a regexp heuristic. To be safe, always
       put a space after the # sign to make sure it is treated as a comment.

       The special comment "#include 'filename'" acts like the C preprocessor directive and will
       insert the comments of a named file into the position at which it occurs. Relative paths
       will be treated relative to the file in which the #include occurs. Nested #include
       directives are allowed:

        #include "/usr/local/share/my_directives.txt"
        #include 'my_directives.txt'
        #include chromosome3_features.gff3

       You can enclose the file path in single or double quotes as shown above. If there are no
       spaces in the filename the quotes are optional.

       Include file processing is not very smart. Avoid creating circular #include references.
       You have been warned!

   Caveats
       Note that this loader always creates denormalized features such that subfeatures and their
       parents are stored as one big database object. The GFF3 format and its loader is usually
       preferred for both space and execution efficiency.

METHODS

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

       This method creates a new FeatureFile 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
       FeatureFile 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 "bdb" 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 FeatureFile 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 FeatureFile 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

   default_seqfeature_class
         $class = $loader->default_seqfeature_class

       Return the default SeqFeatureI class (Bio::Graphics::Feature).

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

       Load the FeatureFile 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.

   load_line
           $loader->load_line($data);

       Load a line of a FeatureFile 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
         $loader->handle_feature($gff3_line)

       This method is called to process a single FeatureFile 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.

   parse_attributes
        @attributes = $loader->parse_attributes($attribute_line)

       This method parses the information contained in the $attribute_line into a flattened hash
       (array). It may return one element, in which case it is an implicit

   start_or_finish_sequence
         $loader->start_or_finish_sequence('Chr9')

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

BUGS

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

SEE ALSO

       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::bdb

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.

perl v5.28.0                                201Bio::DB::SeqFeature::Store::FeatureFileLoader(3pm)