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

Provided by: libbio-perl-perl_1.6.924-3_all

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.

AUTHOR