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Summary

Bio::Index::AbstractSeq - base class for AbstractSeq

Package variables

Included modules

Inherit

Bio::DB::SeqI Bio::Index::Abstract

Synopsis

  # Make a new sequence file indexing package

  package MyShinyNewIndexer;

  use base qw(Bio::Index::AbstractSeq);

  # Now provide the necessary methods...

Description

Provides a common base class for multiple sequence files built using
the Bio::Index::Abstract system, and provides a Bio::DB::SeqI
interface.

Methods

Methods description

 Title   : _file_format
 Usage   : $self->_file_format
 Function: Derived classes should override this
           method (it throws an exception here)
           to give the file format of the files used
 Example :
 Returns : 
 Args    :

  Title   : fetch
  Usage   : $index->fetch( $id )
  Function: Returns a Bio::Seq object from the index
  Example : $seq = $index->fetch( 'dJ67B12' )
  Returns : Bio::Seq object
  Args    : ID

  Title   : _get_SeqIO_object
  Usage   : $index->_get_SeqIO_object( $file )
  Function: Returns a Bio::SeqIO object for the file
  Example : $seq = $index->_get_SeqIO_object( 0 )
  Returns : Bio::SeqIO object
  Args    : File number (an integer)

 Title   : get_Seq_by_id
 Usage   : $seq = $db->get_Seq_by_id()
 Function: retrieves a sequence object, identically to
           ->fetch, but here behaving as a Bio::DB::BioSeqI
 Returns : new Bio::Seq object
 Args    : string represents the id

 Title   : get_Seq_by_acc
 Usage   : $seq = $db->get_Seq_by_acc()
 Function: retrieves a sequence object, identically to
           ->fetch, but here behaving as a Bio::DB::BioSeqI
 Returns : new Bio::Seq object
 Args    : string represents the accession number

 Title   : get_PrimarySeq_stream
 Usage   : $stream = get_PrimarySeq_stream
 Function: Makes a Bio::DB::SeqStreamI compliant object
           which provides a single method, next_primary_seq
 Returns : Bio::DB::SeqStreamI
 Args    : none

 Title   : get_all_primary_ids
 Usage   : @ids = $seqdb->get_all_primary_ids()
 Function: gives an array of all the primary_ids of the 
           sequence objects in the database. These
           maybe ids (display style) or accession numbers
           or something else completely different - they
           *are not* meaningful outside of this database
           implementation.
 Example :
 Returns : an array of strings
 Args    : none

 Title   : get_Seq_by_primary_id
 Usage   : $seq = $db->get_Seq_by_primary_id($primary_id_string);
 Function: Gets a Bio::Seq object by the primary id. The primary
           id in these cases has to come from $db->get_all_primary_ids.
           There is no other way to get (or guess) the primary_ids
           in a database.

           The other possibility is to get Bio::PrimarySeqI objects
           via the get_PrimarySeq_stream and the primary_id field
           on these objects are specified as the ids to use here.
 Returns : A Bio::Seq object
 Args    : primary id (as a string)
 Throws  : "acc does not exist" exception

Methods code

sub new {

	my ($class, @args) = @_;
	my $self = $class->SUPER::new(@args);
    
	$self->{'_seqio_cache'} = [];
	return $self;

}

sub _file_format {

   my ($self,@args) = @_;

   my $pkg = ref($self);
   $self->throw("Class '$pkg' must provide a file format method correctly");

}

sub fetch {

	my( $self, $id ) = @_;
	my $db = $self->db();
	my $seq;

	if (my $rec = $db->{ $id }) {
		my ($file, $begin) = $self->unpack_record( $rec );
        
		# Get the (possibly cached) SeqIO object
		my $seqio = $self->_get_SeqIO_object( $file );
		my $fh = $seqio->_fh();

		# move to start of record
		# $begin-- if( $^O =~ /mswin/i); # workaround for Win DB_File bug
		seek($fh, $begin, 0);
	
		$seq = $seqio->next_seq();	
	}

	# we essentially assumme that the primary_id for the database
	# is the display_id
	if (ref($seq) && $seq->isa('Bio::PrimarySeqI') &&
		 $seq->primary_id =~ /^\D+$/) {
		$seq->primary_id( $seq->display_id() );
	}
	return $seq;

}

sub _get_SeqIO_object {

    my( $self, $i ) = @_;
    
    unless ($self->{'_seqio_cache'}[$i]) {
        my $fh = $self->_file_handle($i);
        # make a new SeqIO object
        my $seqio = Bio::SeqIO->new( -Format => $self->_file_format,
				     -fh     => $fh);
        $self->{'_seqio_cache'}[$i] = $seqio;
    }
    return $self->{'_seqio_cache'}[$i];

}

sub get_Seq_by_id {

   my ($self,$id) = @_;

   return $self->fetch($id);

}

sub get_Seq_by_acc {

   my ($self,$id) = @_;

   return $self->fetch($id);

}

sub get_PrimarySeq_stream {

    my $self = shift;
    my $num  = $self->_file_count() || 0;
    my @file;
    
    for (my $i = 0; $i < $num; $i++) {
        my( $file, $stored_size ) = $self->unpack_record( $self->db->{"__FILE_$i"} );
	push(@file,$file);
    }
   
    my $out = Bio::SeqIO::MultiFile->new( '-format' => $self->_file_format , -files =>\@ file);
    return $out;

}

sub get_all_primary_ids {

   my ($self,@args) = @_;
    my $db = $self->db;
   
   # the problem is here that we have indexed things both on
   # accession number and name. 

   # We could take two options
   # here - loop over the database, returning only one copy of each
   # id that points to the same byte position, or we rely on semantics
   # of accession numbers.

   # someone is going to index a database with no accession numbers.
   # doh!. We have to uniquify the index...

   my( %bytepos );
   while (my($id, $rec) = each %$db) {
       if( $id =~ /^__/ ) {
           # internal info
           next;
       }
       my ($file, $begin) = $self->unpack_record( $rec );
       
       $bytepos{"$file:$begin"} = $id;
   }

   return values %bytepos;

}

sub get_Seq_by_primary_id {

   my ($self,$id) = @_;
   return $self->fetch($id);
}

1;

}

General documentation

User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions
preferably to one of the Bioperl mailing lists.
Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:

  https://redmine.open-bio.org/projects/bioperl/

Email birney@ebi.ac.uk

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _

Bio::Index::Abstract, which provides dbm indexing for flat files of
any type, containing sequence or not. Bio::Index::AbstractSeq inherits
from Bio::Index::Abstract