Bio::DB::Fasta3pm

Usage

  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'};

Overview

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.

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:

 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

 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:

 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

 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).

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

 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

 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