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Bio::DB::SeqFeature::SUser:ConBio::DB::SeqFeature::Store::FeatureFileLoader(3)

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 writeable 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 v5.14.1		      Bio::DB::SeqFeature::Store::FeatureFileLoader(3)
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