Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::DB::Fasta - Fast indexed access to fasta files

SYNOPSIS

         use Bio::DB::Fasta;

         # Create database from a directory of Fasta files
         my $db       = Bio::DB::Fasta->new('/path/to/fasta/files/');
         my @ids      = $db->get_all_primary_ids;

         # Simple access
         my $seqstr   = $db->seq('CHROMOSOME_I', 4_000_000 => 4_100_000);
         my $revseq   = $db->seq('CHROMOSOME_I', 4_100_000 => 4_000_000);
         my $length   = $db->length('CHROMOSOME_I');
         my $header   = $db->header('CHROMOSOME_I');
         my $alphabet = $db->alphabet('CHROMOSOME_I');

         # Access to sequence objects. See Bio::PrimarySeqI.
         my $seq     = $db->get_Seq_by_id('CHROMOSOME_I');
         my $seqstr  = $seq->seq;
         my $subseq  = $seq->subseq(4_000_000 => 4_100_000);
         my $trunc   = $seq->trunc(4_000_000 => 4_100_000);
         my $length  = $seq->length;

         # Loop through sequence objects
         my $stream  = $db->get_PrimarySeq_stream;
         while (my $seq = $stream->next_seq) {
           # Bio::PrimarySeqI stuff
         }

         # Filehandle access
         my $fh = Bio::DB::Fasta->newFh('/path/to/fasta/files/');
         while (my $seq = <$fh>) {
           # Bio::PrimarySeqI stuff
         }

         # Tied hash access
         tie %sequences,'Bio::DB::Fasta','/path/to/fasta/files/';
         print $sequences{'CHROMOSOME_I:1,20000'};

DESCRIPTION

       Bio::DB::Fasta provides indexed access to a single Fasta file, several files, or a
       directory of files. It provides persistent random access to each sequence entry (either as
       a Bio::PrimarySeqI-compliant object or a string), and to subsequences within each entry,
       allowing you to retrieve portions of very large sequences without bringing the entire
       sequence into memory. Bio::DB::Fasta is based on Bio::DB::IndexedBase. See this module's
       documentation for details.

       The Fasta files may contain any combination of nucleotide and protein sequences; during
       indexing the module guesses the molecular type. 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.

       The module uses /^>(\S+)/ to extract the primary ID of each sequence from the Fasta
       header. See -makeid in Bio::DB::IndexedBase to pass a callback routine to reversibly
       modify this primary ID, e.g. if you wish to extract a specific portion of the
       gi|gb|abc|xyz GenBank IDs.

DATABASE CREATION AND INDEXING

       The object-oriented constructor is new(), the filehandle constructor is newFh() and the
       tied hash constructor is tie(). They all allow one to index a single Fasta file, several
       files, or a directory of files. See Bio::DB::IndexedBase.

SEE ALSO

       Bio::DB::IndexedBase

       Bio::DB::Qual

       Bio::PrimarySeqI

AUTHOR

       Lincoln Stein <lstein@cshl.org>.

       Copyright (c) 2001 Cold Spring Harbor Laboratory.

       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 _

       For BioPerl-style access, the following methods are provided:

   get_Seq_by_id
        Title   : get_Seq_by_id, get_Seq_by_acc, 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.
        Returns : A Bio::PrimarySeq::Fasta object (Bio::PrimarySeqI compliant)
                  Note that to save resource, Bio::PrimarySeq::Fasta sequence objects
                  only load the sequence string into memory when requested using seq().
                  See L<Bio::PrimarySeqI> for methods provided by the sequence objects
                  returned from get_Seq_by_id() and get_PrimarySeq_stream().
        Args    : ID

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

       For simple access, the following methods are provided:

   new
        Title   : new
        Usage   : my $db = Bio::DB::Fasta->new( $path, %options);
        Function: Initialize a new database object. When indexing a directory, files
                  ending in .fa,fasta,fast,dna,fna,faa,fsa are indexed by default.
        Returns : A new Bio::DB::Fasta object.
        Args    : A single file, or path to dir, or arrayref of files
                  Optional arguments: see Bio::DB::IndexedBase

   seq
        Title   : seq, sequence, subseq
        Usage   : # Entire sequence string
                  my $seqstr    = $db->seq($id);
                  # Subsequence
                  my $subseqstr = $db->seq($id, $start, $stop, $strand);
                  # or...
                  my $subseqstr = $db->seq($compound_id);
        Function: Get a subseq of a sequence from the database. For your convenience,
                  the sequence to extract can be specified with any of the following
                  compound IDs:
                     $db->seq("$id:$start,$stop")
                     $db->seq("$id:$start..$stop")
                     $db->seq("$id:$start-$stop")
                     $db->seq("$id:$start,$stop/$strand")
                     $db->seq("$id:$start..$stop/$strand")
                     $db->seq("$id:$start-$stop/$strand")
                     $db->seq("$id/$strand")
                  In the case of DNA or RNA sequence, if $stop is less than $start,
                  then the reverse complement of the sequence is returned. Avoid using
                  it if possible since this goes against Bio::Seq conventions.
        Returns : A string
        Args    : ID of sequence to retrieve
                    or
                  Compound ID of subsequence to fetch
                    or
                  ID, optional start (defaults to 1), optional end (defaults to length
                  of sequence) and optional strand (defaults to 1).

   length
        Title   : length
        Usage   : my $length = $qualdb->length($id);
        Function: Get the number of residues in the indicated sequence.
        Returns : Number
        Args    : ID of entry

   header
        Title   : header
        Usage   : my $header = $db->header($id);
        Function: Get the header line (ID and description fields) of the specified
                  sequence.
        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