Bio::DB::SeqFeature::Store GFF2Loader
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Summary
Bio::DB::SeqFeature::Store::GFF2Loader -- GFF2 file loader for Bio::DB::SeqFeature::Store
Package variables
Privates (from "my" definitions)
%Special_attributes = ( Gap => 1, Target => 1, Parent => 1, Name => 1, Alias => 1, ID => 1, index => 1, Index => 1, )
Included modules
Bio::DB::GFF::Util::Rearrange
Carp ' croak '
Text::ParseWords ' quotewords '
Inherit
Bio::DB::SeqFeature::Store::GFF3Loader
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.
Methods
parse_attributes
No description
Code
Methods description
None available.
Methods code
parse_attributesdescriptionprevnextTop
sub parse_attributes {
 # overridden  my $self = shift;
my $att = shift; my @groups = quotewords('\s*;\s*',0,$att); my (%reserved,%unreserved); my $found_name; for (@groups) { my ($tag,$value); if (/^(\S+)\s+(.+)/) { # Tag value pair
($tag,$value) = ($1,$2); } else { $tag = 'Note'; $value = $_; } if ($tag eq 'Target') { my ($target,$start,$end) = split /\s+/,$value; push @{$reserved{ID}},$target; $found_name++; if ($start <= $end) { $value .= ' +' } else { $value .= ' -' } } if (!$found_name++) { push @{$reserved{Alias}},$value; $value = "$tag:$value"; push @{$reserved{ID}},$value; $tag = 'Name'; } if ($Special_attributes{$tag}) { # reserved attribute
push @{$reserved{$tag}},$value; } else { push @{$unreserved{$tag}},$value; } } return (\%reserved,\%unreserved);
}
General documentation
newTop
 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.
loadTop
 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.
accessorsTop
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 MethodsTop
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).
BUGSTop
This is an early version, so there are certainly some bugs. Please
use the BioPerl bug tracking system to report bugs.
SEE ALSOTop
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
AUTHORTop
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.