Bio::DB::Qual(3) 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 to index a single Fasta file, several files, or a directory of files. See Bio::DB::IndexedBase.

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

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