Bio::DB::SeqFeature::Store::memory man page on Fedora

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Bio::DB::SeqFeature::SUser:Contributed PeBio::DB::SeqFeature::Store::memory(3)

NAME
       Bio::DB::SeqFeature::Store::memory -- In-memory implementation of
       Bio::DB::SeqFeature::Store

SYNOPSIS
	 use Bio::DB::SeqFeature::Store;

	 # Open the sequence database
	 my $db	     = Bio::DB::SeqFeature::Store->new( -adaptor => 'memory',
							-dsn	 => '/var/databases/test');

	 # search... by id
	 my @features = $db->fetch_many(@list_of_ids);

	 # ...by name
	 @features = $db->get_features_by_name('ZK909');

	 # ...by alias
	 @features = $db->get_features_by_alias('sma-3');

	 # ...by type
	 @features = $db->get_features_by_name('gene');

	 # ...by location
	 @features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000);

	 # ...by attribute
	 @features = $db->get_features_by_attribute({description => 'protein kinase'})

	 # ...by the GFF "Note" field
	 @result_list = $db->search_notes('kinase');

	 # ...by arbitrary combinations of selectors
	 @features = $db->features(-name => $name,
				   -type => $types,
				   -seq_id => $seqid,
				   -start  => $start,
				   -end	   => $end,
				   -attributes => $attributes);

	 # ...using an iterator
	 my $iterator = $db->get_seq_stream(-name => $name,
					    -type => $types,
					    -seq_id => $seqid,
					    -start  => $start,
					    -end    => $end,
					    -attributes => $attributes);

	 while (my $feature = $iterator->next_seq) {
	   # do something with the feature
	 }

	 # ...limiting the search to a particular region
	 my $segment  = $db->segment('Chr1',5000=>6000);
	 my @features = $segment->features(-type=>['mRNA','match']);

	 # getting & storing sequence information
	 # Warning: this returns a string, and not a PrimarySeq object
	 $db->insert_sequence('Chr1','GATCCCCCGGGATTCCAAAA...');
	 my $sequence = $db->fetch_sequence('Chr1',5000=>6000);

	 # what feature types are defined in the database?
	 my @types    = $db->types;

	 # create a new feature in the database
	 my $feature = $db->new_feature(-primary_tag => 'mRNA',
					-seq_id	     => 'chr3',
					-start	    => 10000,
					-end	    => 11000);

DESCRIPTION
       Bio::DB::SeqFeature::Store::memory is the in-memory adaptor for
       Bio::DB::SeqFeature::Store. You will not create it directly, but
       instead use Bio::DB::SeqFeature::Store->new() to do so.

       See Bio::DB::SeqFeature::Store for complete usage instructions.

   Using the memory adaptor
       Before using the memory adaptor, populate a readable-directory on the
       file system with annotation and/or sequence files. The annotation files
       must be in GFF3 format, and shold end in the extension .gff or .gff3.
       They may be compressed with "compress", "gzip" or "bzip2" (in which
       case the appropriate compression extension must be present as well.)

       You may include sequence data inline in the GFF3 files, or put the
       sequence data in one or more separate FASTA-format files. These files
       must end with .fa or .fasta and may be compressed. Because of the way
       the adaptor works, you will get much better performance if you keep the
       sequence data in separate FASTA files.

       Initialize the database using the -dsn option. This should point to the
       directory creating the annotation and sequence files, or to a single
       GFF3 file. Examples:

	 # load all GFF3 and FASTA files located in /var/databases/test directory
	 $db  = Bio::DB::SeqFeature::Store->new( -adaptor => 'memory',
						 -dsn	  => '/var/databases/test');

	 # load the data in a single compressed GFF3 file located at
	 # /usr/annotations/worm.gf33.gz
	 $db  = Bio::DB::SeqFeature::Store->new( -adaptor => 'memory',
						 -dsn	  => '/usr/annotations/worm.gff3.gz');

       For compatibility with the Bio::DB::GFF memory adapter, -gff is
       recognized as an alias for -dsn.

       See Bio::DB::SeqFeature::Store for all the access methods supported by
       this adaptor. The various methods for storing and updating features and
       sequences into the database are supported, including GFF3 loading
       support, but since this is an in-memory adaptor all changes you make
       will be lost when the script exits.

   types
	Title	: types
	Usage	: @type_list = $db->types
	Function: Get all the types in the database
	Returns : array of Bio::DB::GFF::Typename objects (arrayref in scalar context)
	Args	: none
	Status	: public

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, Bio::DB::SeqFeature::Store,
       Bio::DB::SeqFeature::GFF3Loader, Bio::DB::SeqFeature::Segment,
       Bio::DB::SeqFeature::Store::berkeleydb,
       Bio::DB::SeqFeature::Store::DBI::mysql

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			  2011-07Bio::DB::SeqFeature::Store::memory(3)
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