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man : Bio::DB::SeqFeature::Store::GFF2Loader(3p)
Bio::DB::SeqFeature::Store::GFF2Loader(3) User Contributed Perl Documentation
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 accomodate
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 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 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 <lsteinATcshl.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 v5.12.2 February 24, 2011
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