NAME

       Bio::DB::Qual - Fast indexed access to quality files

SYNOPSIS

         use Bio::DB::Qual;

         # create database from directory of qual files
         my $db      = Bio::DB::Qual->new('/path/to/qual/files/');
         my @ids     = $db->get_all_primary_ids;

         # Simple access
         my @qualarr = @{$db->qual('CHROMOSOME_I',4_000_000 => 4_100_000)};
         my @revqual = @{$db->qual('CHROMOSOME_I',4_100_000 => 4_000_000)};
         my $length  = $db->length('CHROMOSOME_I');
         my $header  = $db->header('CHROMOSOME_I');

         # Access to sequence objects. See Bio::PrimarySeqI.
         my $obj     = $db->get_Qual_by_id('CHROMOSOME_I');
         my @qual    = @{$obj->qual};
         my @subqual = @{$obj->subqual(4_000_000 => 4_100_000)};
         my $length  = $obj->length;

         # Loop through sequence objects
         my $stream  = $db->get_PrimarySeq_stream;
         while (my $qual = $stream->next_seq) {
           # Bio::Seq::PrimaryQual operations
         }

         # Filehandle access
         my $fh = Bio::DB::Qual->newFh('/path/to/qual/files/');
         while (my $qual = <$fh>) {
           # Bio::Seq::PrimaryQual operations
         }

         # Tied hash access
         tie %qualities,'Bio::DB::Qual','/path/to/qual/files/';
         print $qualities{'CHROMOSOME_I:1,20000'};

DESCRIPTION

       Bio::DB::Qual provides indexed access to a single Fasta file, several files, or a directory of files. It
       provides random access to each quality score entry without having to read the file from the beginning.
       Access to subqualities (portions of a quality score) is provided, although contrary to Bio::DB::Fasta,
       the full quality score has to be brought in memory. Bio::DB::Qual is based on Bio::DB::IndexedBase. See
       this module's documentation for details.

       The qual files should contain decimal quality scores. Entries may have any line length up to 65,536
       characters, and different line lengths are allowed in the same file. However, within a quality score
       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 quality score from the qual 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::Fasta

       Bio::Seq::PrimaryQual

LIMITATIONS

       When a quality score is deleted from one of the qual 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. Currently, the only way to accommodate deletions is to rebuild the entire index,
       either by deleting it manually, or by passing -reindex=>1 to new() when initializing the module.

       All quality score lines for a given quality score must have the same length except for the last (not sure
       why there is this limitation). This is not problematic for sequences but could be annoying for quality
       scores. A workaround is to make sure that your quality scores fit on no more than 2 lines. Another
       solution could be to padd them with blank spaces so that each line has the same number of characters
       (maybe this padding should be implemented in Bio::SeqIO::qual?).

AUTHOR

       Florent E Angly <florent . angly @ gmail-dot-com>.

       Module largely based on and adapted from Bio::DB::Fasta by Lincoln Stein.

       Copyright (c) 2007 Florent E Angly.

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl
       itself.

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_version, get_Seq_by_primary_id,
                  get_Qual_by_id, get_qual_by_acc, get_qual_by_version, get_qual_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_Seq_stream, get_PrimarySeq_stream
        Usage   : my $stream = $db->get_Seq_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::Qual->new( $path, %options);
        Function: Initialize a new database object. When indexing a directory, files
                  ending in .qual,qa are indexed by default.
        Returns : A new Bio::DB::Qual object
        Args    : A single file, or path to dir, or arrayref of files
                  Optional arguments: see Bio::DB::IndexedBase

   qual
        Title   : qual, quality, subqual
        Usage   : # All quality scores
                  my @qualarr = @{$qualdb->subqual($id)};
                  # Subset of the quality scores
                  my @subqualarr = @{$qualdb->subqual($id, $start, $stop, $strand)};
                  # or...
                  my @subqualarr = @{$qualdb->subqual($compound_id)};
        Function: Get a subqual of an entry in the database. For your convenience,
                  the sequence to extract can be specified with any of the following
                  compound IDs:
                     $db->qual("$id:$start,$stop")
                     $db->qual("$id:$start..$stop")
                     $db->qual("$id:$start-$stop")
                     $db->qual("$id:$start,$stop/$strand")
                     $db->qual("$id:$start..$stop/$strand")
                     $db->qual("$id:$start-$stop/$strand")
                     $db->qual("$id/$strand")
                  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 : Reference to an array of quality scores
        Args    : Compound ID of entry to retrieve
                    or
                  ID, optional start (defaults to 1), optional end (defaults to the
                  number of quality scores for this sequence), and strand (defaults to
                  1).

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