Provided by: libbio-perl-perl_1.7.8-1_all bug

NAME

       Bio::DB::IndexedBase - Base class for modules using indexed sequence files

SYNOPSIS

         use Bio::DB::XXX; # a made-up class that uses Bio::IndexedBase

         # 1/ Bio::SeqIO-style access

         # Index some sequence files
         my $db = Bio::DB::XXX->new('/path/to/file');    # from a single file
         my $db = Bio::DB::XXX->new(['file1', 'file2']); # from multiple files
         my $db = Bio::DB::XXX->new('/path/to/files/');  # from a directory

         # Get IDs of all the sequences in the database
         my @ids = $db->get_all_primary_ids;

         # Get a specific sequence
         my $seq = $db->get_Seq_by_id('CHROMOSOME_I');

         # Loop through all sequences
         my $stream = $db->get_PrimarySeq_stream;
         while (my $seq = $stream->next_seq) {
           # Do something...
         }

         # 2/ Access via filehandle
         my $fh = Bio::DB::XXX->newFh('/path/to/file');
         while (my $seq = <$fh>) {
           # Do something...
         }

         # 3/ Tied-hash access
         tie %sequences, 'Bio::DB::XXX', '/path/to/file';
         print $sequences{'CHROMOSOME_I:1,20000'};

DESCRIPTION

       Bio::DB::IndexedBase provides a base class for modules that want to index and read
       sequence files and provides persistent, random access to each sequence entry, without
       bringing the entire file into memory. This module is compliant with the Bio::SeqI
       interface and both. Bio::DB::Fasta and Bio::DB::Qual both use Bio::DB::IndexedBase.

       When you initialize the module, you point it at a single file, several files, or a
       directory of files. The first time it is run, the module generates an index of the content
       of the files using the AnyDBM_File module (BerkeleyDB preferred, followed by GDBM_File,
       NDBM_File, and SDBM_File). Subsequently, it uses the index file to find the sequence file
       and offset for any requested sequence. If one of the source files is updated, the module
       reindexes just that one file. You can also force reindexing manually at any time. For
       improved performance, the module keeps a cache of open filehandles, closing less-recently
       used ones when the cache is full.

       Entries may have any line length up to 65,536 characters, and different line lengths are
       allowed in the same file.  However, within a sequence entry, all lines must be the same
       length except for the last. An error will be thrown if this is not the case!

       This module was developed for use with the C. elegans and human genomes, and has been
       tested with sequence segments as large as 20 megabases. Indexing the C.  elegans genome
       (100 megabases of genomic sequence plus 100,000 ESTs) takes ~5 minutes on my 300 MHz
       pentium laptop. On the same system, average access time for any 200-mer within the C.
       elegans genome was <0.02s.

DATABASE CREATION AND INDEXING

       The two constructors for this class are new() and newFh(). The former creates a
       Bio::DB::IndexedBase object which is accessed via method calls. The latter creates a tied
       filehandle which can be used Bio::SeqIO style to fetch sequence objects in a stream
       fashion. There is also a tied hash interface.

       $db = Bio::DB::IndexedBase->new($path [,%options])
           Create a new Bio::DB::IndexedBase object from the files designated by $path $path may
           be a single file, an arrayref of files, or a directory containing such files.

           After the database is created, you can use methods like get_all_primary_ids() and
           get_Seq_by_id() to retrieve sequence objects.

       $fh = Bio::DB::IndexedBase->newFh($path [,%options])
           Create a tied filehandle opened on a Bio::DB::IndexedBase object. Reading from this
           filehandle with <> will return a stream of sequence objects, Bio::SeqIO style. The
           path and the options should be specified as for new().

       $obj = tie %db,'Bio::DB::IndexedBase', '/path/to/file' [,@args]
           Create a tied-hash by tieing %db to Bio::DB::IndexedBase using the indicated path to
           the files. The optional @args list is the same set used by new(). If successful, tie()
           returns the tied object, undef otherwise.

           Once tied, you can use the hash to retrieve an individual sequence by its ID, like
           this:

             my $seq = $db{CHROMOSOME_I};

           The keys() and values() functions will return the sequence IDs and their sequences,
           respectively.  In addition, each() can be used to iterate over the entire data set:

            while (my ($id,$sequence) = each %db) {
               print "$id => $sequence\n";
            }

           When dealing with very large sequences, you can avoid bringing them into memory by
           calling each() in a scalar context.  This returns the key only.  You can then use
           tied(%db) to recover the Bio::DB::IndexedBase object and call its methods.

            while (my $id = each %db) {
               print "$id: $db{$sequence:1,100}\n";
               print "$id: ".tied(%db)->length($id)."\n";
            }

           In addition, you may invoke the FIRSTKEY and NEXTKEY tied hash methods directly to
           retrieve the first and next ID in the database, respectively. This allows one to write
           the following iterative loop using just the object-oriented interface:

            my $db = Bio::DB::IndexedBase->new('/path/to/file');
            for (my $id=$db->FIRSTKEY; $id; $id=$db->NEXTKEY($id)) {
               # do something with sequence
            }

INDEX CONTENT

       Several attributes of each sequence are stored in the index file. Given a sequence ID,
       these attributes can be retrieved using the following methods:

       offset($id)
           Get the offset of the indicated sequence from the beginning of the file in which it is
           located. The offset points to the beginning of the sequence, not the beginning of the
           header line.

       strlen($id)
           Get the number of characters in the sequence string.

       length($id)
           Get the number of residues of the sequence.

       linelen($id)
           Get the length of the line for this sequence. If the sequence is wrapped, then
           linelen() is likely to be much shorter than strlen().

       headerlen($id)
           Get the length of the header line for the indicated sequence.

       header_offset
           Get the offset of the header line for the indicated sequence from the beginning of the
           file in which it is located. This attribute is not stored. It is calculated from
           offset() and headerlen().

       alphabet($id)
           Get the molecular type (alphabet) of the indicated sequence. This method handles
           residues according to the IUPAC convention.

       file($id)
           Get the the name of the file in which the indicated sequence can be found.

INTERFACE COMPLIANCE NOTES

       Bio::DB::IndexedBase is compliant with the Bio::DB::SeqI and hence with the
       Bio::RandomAccessI interfaces.

       Database do not necessarily provide any meaningful internal primary ID for the sequences
       they store. However, Bio::DB::IndexedBase's internal primary IDs are the IDs of the
       sequences. This means that the same ID passed to get_Seq_by_id() and
       get_Seq_by_primary_id() will return the same sequence.

       Since this database index has no notion of sequence version or namespace, the
       get_Seq_by_id(), get_Seq_by_acc() and get_Seq_by_version() are identical.

BUGS

       When a sequence is deleted from one of the files, this deletion is not detected by the
       module and removed from the index. As a result, a "ghost" entry will remain in the index
       and will return garbage results if accessed.

       Also, if you are indexing a directory, it is wise to not add or remove files from it.

       In case you have changed the files in a directory, or the sequences in a file, you can to
       rebuild the entire index, either by deleting it manually, or by passing -reindex=>1 to
       new() when initializing the module.

SEE ALSO

       DB_File

       Bio::DB::Fasta

       Bio::DB::Qual

AUTHOR

       Lincoln Stein <lstein@cshl.org>.

       Copyright (c) 2001 Cold Spring Harbor Laboratory.

       Florent Angly (for the modularization)

       This library is free software; you can redistribute it and/or modify it under the same
       terms as Perl itself.  See DISCLAIMER.txt for disclaimers of warranty.

APPENDIX

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

   new
        Title   : new
        Usage   : my $db = Bio::DB::IndexedBase->new($path, -reindex => 1);
        Function: Initialize a new database object
        Returns : A Bio::DB::IndexedBase object
        Args    : A single file, or path to dir, or arrayref of files
                  Optional arguments:

        Option        Description                                         Default
        -----------   -----------                                         -------
        -glob         Glob expression to search for files in directories  *
        -makeid       A code subroutine for transforming IDs              None
        -maxopen      Maximum size of filehandle cache                    32
        -debug        Turn on status messages                             0
        -reindex      Force the index to be rebuilt                       0
        -dbmargs      Additional arguments to pass to the DBM routine     None
        -index_name   Name of the file that will hold the indices
        -clean        Remove the index file when finished                 0

       The -dbmargs option can be used to control the format of the index. For example, you can
       pass $DB_BTREE to this argument so as to force the IDs to be sorted and retrieved
       alphabetically. Note that you must use the same arguments every time you open the index!

       The -makeid option gives you a chance to modify sequence IDs during indexing.  For
       example, you may wish to extract a portion of the gi|gb|abc|xyz nonsense that GenBank
       Fasta files use. The original header line can be recovered later.  The option value for
       -makeid should be a code reference that takes a scalar argument (the full header line) and
       returns a scalar or an array of scalars (the ID or IDs you want to assign). For example:

         $db = Bio::DB::IndexedBase->new('file.fa', -makeid => \&extract_gi);

         sub extract_gi {
             # Extract GI from GenBank
             my $header = shift;
             my ($id) = ($header =~ /gi\|(\d+)/m);
             return $id || '';
         }

       extract_gi() will be called with the full header line, e.g. a Fasta line would include the
       ">", the ID and the description:

        >gi|352962132|ref|NG_030353.1| Homo sapiens sal-like 3 (Drosophila) (SALL3)

       In the database, this sequence can now be retrieved by its GI instead of its complete ID:

        my $seq = $db->get_Seq_by_id(352962132);

       The -makeid option is ignored after the index is constructed.

   newFh
        Title   : newFh
        Usage   : my $fh = Bio::DB::IndexedBase->newFh('/path/to/files/', %options);
        Function: Index and get a new Fh for a single file, several files or a directory
        Returns : Filehandle object
        Args    : Same as new()

   dbmargs
        Title   : dbmargs
        Usage   : my @args = $db->dbmargs;
        Function: Get stored dbm arguments
        Returns : Array
        Args    : None

   glob
        Title   : glob
        Usage   : my $glob = $db->glob;
        Function: Get the expression used to match files in directories
        Returns : String
        Args    : None

   index_dir
        Title   : index_dir
        Usage   : $db->index_dir($dir);
        Function: Index the files that match -glob in the given directory
        Returns : Hashref of offsets
        Args    : Dirname
                  Boolean to force a reindexing the directory

   get_all_primary_ids
        Title   : get_all_primary_ids, get_all_ids, ids
        Usage   : my @ids = $db->get_all_primary_ids;
        Function: Get the IDs stored in all indexes. This is a Bio::DB::SeqI method
                  implementation. Note that in this implementation, the internal
                  database primary IDs are also the sequence IDs.
        Returns : List of ids
        Args    : None

   index_file
        Title   : index_file
        Usage   : $db->index_file($filename);
        Function: Index the given file
        Returns : Hashref of offsets
        Args    : Filename
                  Boolean to force reindexing the file

   index_files
        Title   : index_files
        Usage   : $db->index_files(\@files);
        Function: Index the given files
        Returns : Hashref of offsets
        Args    : Arrayref of filenames
                  Boolean to force reindexing the files

   index_name
        Title   : index_name
        Usage   : my $indexname = $db->index_name($path);
        Function: Get the full name of the index file
        Returns : String
        Args    : None

   path
        Title   : path
        Usage   : my $path = $db->path($path);
        Function: When a single file or a directory of files is indexed, this returns
                  the file directory. When indexing an arbitrary list of files, the
                  return value is the path of the current working directory.
        Returns : String
        Args    : None

   get_PrimarySeq_stream
        Title   : get_PrimarySeq_stream
        Usage   : my $stream = $db->get_PrimarySeq_stream();
        Function: Get a SeqIO-like stream of sequence objects. The stream supports a
                  single method, next_seq(). Each call to next_seq() returns a new
                  PrimarySeqI compliant sequence object, until no more sequences remain.
                  This is a Bio::DB::SeqI method implementation.
        Returns : A Bio::DB::Indexed::Stream object
        Args    : None

   get_Seq_by_id
        Title   : get_Seq_by_id, get_Seq_by_acc, get_Seq_by_version, get_Seq_by_primary_id
        Usage   : my $seq = $db->get_Seq_by_id($id);
        Function: Given an ID, fetch the corresponding sequence from the database.
                  This is a Bio::DB::SeqI and Bio::DB::RandomAccessI method implementation.
        Returns : A sequence object
        Args    : ID

   _calculate_offsets
        Title   : _calculate_offsets
        Usage   : $db->_calculate_offsets($filename, $offsets);
        Function: This method calculates the sequence offsets in a file based on ID and
                  should be implemented by classes that use Bio::DB::IndexedBase.
        Returns : Hash of offsets
        Args    : File to process
                  Hashref of file offsets keyed by IDs.

   offset
        Title   : offset
        Usage   : my $offset = $db->offset($id);
        Function: Get the offset of the indicated sequence from the beginning of the
                  file in which it is located. The offset points to the beginning of
                  the sequence, not the beginning of the header line.
        Returns : String
        Args    : ID of sequence

   strlen
        Title   : strlen
        Usage   : my $length = $db->strlen($id);
        Function: Get the number of characters in the sequence string.
        Returns : Integer
        Args    : ID of sequence

   length
        Title   : length
        Usage   : my $length = $db->length($id);
        Function: Get the number of residues of the sequence.
        Returns : Integer
        Args    : ID of sequence

   linelen
        Title   : linelen
        Usage   : my $linelen = $db->linelen($id);
        Function: Get the length of the line for this sequence.
        Returns : Integer
        Args    : ID of sequence

   headerlen
        Title   : headerlen
        Usage   : my $length = $db->headerlen($id);
        Function: Get the length of the header line for the indicated sequence.
        Returns : Integer
        Args    : ID of sequence

   header_offset
        Title   : header_offset
        Usage   : my $offset = $db->header_offset($id);
        Function: Get the offset of the header line for the indicated sequence from
                  the beginning of the file in which it is located.
        Returns : String
        Args    : ID of sequence

   alphabet
        Title   : alphabet
        Usage   : my $alphabet = $db->alphabet($id);
        Function: Get the molecular type of the indicated sequence: dna, rna or protein
        Returns : String
        Args    : ID of sequence

   file
        Title   : file
        Usage   : my $file = $db->file($id);
        Function: Get the the name of the file in which the indicated sequence can be
                  found.
        Returns : String
        Args    : ID of sequence