Bio::DB::SeqFeature::Store::GFF3Loader Bio::DB::SeqFeature::Store::GFF3Loader is a GFF3 file loader for Bio::DB::SeqFeature::Store.
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Perl module Loader GFF3 loader GFF3

Bio::DB::SeqFeature::Store::GFF3Loader Description

Bio::DB::SeqFeature::Store::GFF3Loader is a GFF3 file loader for Bio::DB::SeqFeature::Store. Bio::DB::SeqFeature::Store::GFF3Loader is a GFF3 file loader for Bio::DB::SeqFeature::Store.SYNOPSIS use Bio::DB::SeqFeature::Store; # 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::GFF3Loader->new(-store => $db, -verbose => 1, -fast => 1); $loader->load('./my_genome.gff3');The Bio::DB::SeqFeature::Store::GFF3Loader object parsers GFF3-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 GFF3 databases by a factor of 5-10.The GFF3 file format has been extended very slightly to accomodate Bio::DB::SeqFeature::Store. First, the loader recognizes is a new directive: # #index-subfeatures Note that you can place a space between the two #'s in order to prevent GFF3 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=1You can use this to turn indexing on and off, overriding the default for a particular feature.new Title : new Usage : $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(@options) Function: create a new parser Returns : a Bio::DB::SeqFeature::Store::GFF3Loader gff3 parser and loader Args : several - see below Status : publicThis method creates a new GFF3 loader and establishes its connection with a Bio::DB::SeqFeature::Store database. Arguments are -name=>$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.Requirements:· Perl Requirements: · Perl

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