view variant_effect_predictor/Bio/Index/AbstractSeq.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

# $Id: AbstractSeq.pm,v 1.16 2002/10/22 07:38:33 lapp Exp $
#
# BioPerl module for Bio::DB::AbstractSeq
#
# Cared for by Ewan Birney <[e-mail]>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::Index::AbstractSeq - Base class for AbstractSeq s 

=head1 SYNOPSIS

  # Make a new sequence file indexing package

  package MyShinyNewIndexer;
  use Bio::Index::AbstractSeq;

  @ISA = ('Bio::Index::AbstractSeq');

  # Now provide the necessary methods...

=head1 DESCRIPTION

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

=head1 FEEDBACK

=head2 Mailing Lists

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.

  [e-mail]             - General discussion
  http://bioperl.org/MailList.shtml - About the mailing lists

=head2 Reporting Bugs

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

  [e-mail]
  http://bugzilla.bioperl.org/

=head1 AUTHOR - Ewan Birney

Email [e-mail]

Describe contact details here

=head1 APPENDIX

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

=head1 SEE ALSO

Bio::Index::Abstract - Module which
Bio::Index::AbstractSeq inherits off, which
provides dbm indexing for flat files (which are
not necessarily sequence files).

=cut

# Let's begin the code ...


package Bio::Index::AbstractSeq;
use vars qw(@ISA);
use strict;

use Bio::SeqIO::MultiFile;
use Bio::Index::Abstract;
use Bio::DB::SeqI;


@ISA = qw(Bio::Index::Abstract Bio::DB::SeqI);

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

=head2 _file_format

 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    :


=cut

sub _file_format {
   my ($self,@args) = @_;

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

=head2 fetch

  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

=cut

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
    $seq->primary_id($seq->display_id()) if( defined $seq && ref($seq) &&
					     $seq->isa('Bio::PrimarySeqI') );

    return $seq;
}

=head2 _get_SeqIO_object

  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)

=cut

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];
}

=head2 get_Seq_by_id

 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


=cut

sub get_Seq_by_id {
   my ($self,$id) = @_;

   return $self->fetch($id);
}

=head2 get_Seq_by_acc

 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


=cut

sub get_Seq_by_acc {
   my ($self,$id) = @_;

   return $self->fetch($id);
}

=head2 get_PrimarySeq_stream

 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


=cut

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;
}

=head2 get_all_primary_ids

 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


=cut

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;
}


=head2 get_Seq_by_primary_id

 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


=cut

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

1;