Bio::DB Qual
Other packages in the module: Bio::DB::Qual
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Summary
Bio::DB::Qual - Fast indexed access to quality files
Package variables
No package variables defined.
Included modules
File::Spec
IO::File
Inherit
Bio::DB::IndexedBase
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.
Methods
_calculate_offsets
No description
Code
get_PrimaryQual_stream
No description
Code
get_Qual_by_id
No description
Code
subqual
No description
Code
headerDescriptionCode
FETCH
No description
Code
Methods description
headercode    nextTop
 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
Methods code
_calculate_offsetsdescriptionprevnextTop
sub _calculate_offsets {
    # Bio::DB::IndexedBase calls this to calculate offsets
my ($self, $fileno, $file, $offsets) = @_; my $fh = IO::File->new($file) or $self->throw("Could not open $file: $!"); binmode $fh; warn "Indexing $file\n" if $self->{debug}; my ($offset, @ids, $linelen, $headerlen, $count, $qual_lines, $last_line, $numres, %offsets); my ($l3_len, $l2_len, $l_len, $blank_lines) = (0, 0, 0, 0); my $termination_length = $self->{termination_length}; while (my $line = <$fh>) { # Account for crlf-terminated Windows files
if (index($line, '>') == 0) { if ($line =~ /^>(\S+)/) { print STDERR "Indexed $count quality scores...\n" if $self->{debug} && (++$count%1000) == 0; $self->_check_linelength($linelen); my $pos = tell($fh); if (@ids) { my $strlen = $pos - $offset - length($line); $strlen -= $termination_length * $qual_lines; my $ppos = &{$self->{packmeth}}($offset, $strlen, $numres, $linelen, $headerlen, Bio::DB::IndexedBase::NA, $fileno); for my $id (@ids) { $offsets->{$id} = $ppos; } $numres = 0; } @ids = $self->_makeid($line); ($offset, $headerlen, $linelen, $qual_lines) = ($pos, length $line, 0, 0); ($l3_len, $l2_len, $l_len, $blank_lines) = (0, 0, 0, 0); } else { # Catch bad header lines, bug 3172
$self->throw("FASTA header doesn't match '>(\\S+)': $line"); } } elsif ($line !~ /\S/) { # Skip blank line
$blank_lines++; next; } else { # Need to check every line :(
$l3_len = $l2_len; $l2_len = $l_len; $l_len = length $line; if (Bio::DB::IndexedBase::DIE_ON_MISSMATCHED_LINES) { if ( ($l3_len > 0) && ($l2_len > 0) && ($l3_len != $l2_len) ) { my $fap = substr($line, 0, 20).".."; $self->throw("Each line of the qual entry must be the same ". "length except the last. Line above #$. '$fap' is $l2_len". " != $l3_len chars."); } if ($blank_lines) { # Blank lines not allowed in entry
$self->throw("Blank lines can only precede header lines, ". "found preceding line #$."); } } $linelen ||= length $line; $qual_lines++; $numres += scalar split /\s+/, $line; } $last_line = $line; } # Process last entry
$self->_check_linelength($linelen); my $pos = tell($fh); if (@ids) { my $strlen = $pos - $offset; if ($linelen == 0) { $strlen = 0; } else { if ($last_line !~ /\s$/) { $qual_lines--; } $strlen -= $termination_length * $qual_lines; } my $ppos = &{$self->{packmeth}}($offset, $strlen, $numres, $linelen, $headerlen, Bio::DB::IndexedBase::NA, $fileno); for my $id (@ids) { $offsets->{$id} = $ppos; } } return\% offsets; } # for backward compatibility
}
get_PrimaryQual_streamdescriptionprevnextTop
sub get_PrimaryQual_stream {
   my $self = shift;
   return $self->get_PrimarySeq_stream;
}


# for backward compatibility
}
get_Qual_by_iddescriptionprevnextTop
sub get_Qual_by_id {
    my ($self, $id) = @_;
    return $self->get_Seq_by_id($id);
}

*get_qual_by_version = *get_qual_by_primary_id = *get_qual_by_acc =\& get_Qual_by_id;
}
subqualdescriptionprevnextTop
sub subqual {
    my ($self, $id, $start, $stop, $strand) = @_;

    # Quality values in a quality score can have 1 or 2 digits and are separated
# by one (or several?) spaces. Thus contrary to Bio::DB::Fasta, here there
# is no easy way match the position of a quality value to its position in
# the quality string.
# As a consequence, if a subqual of the quality is requested, we still need
# to grab the full quality string first - performance penalty for big
# quality scores :(
# I think there is no way around starting at the begining of the quality
# score but maybe there is a resource-efficient way of starting at the
# begining of the quality score and stopping when the the position of the
# last quality value requested is reached??
$self->throw('Need to provide a sequence ID') if not defined $id; ($id, $start, $stop, $strand) = $self->_parse_compound_id($id, $start, $stop, $strand); # Position in quality string
my $string_start = 1; my $string_stop = $self->strlen($id); # Fetch full quality string
my $fh = $self->_fh($id) or return; my $filestart = $self->_calc_offset($id, $string_start); my $filestop = $self->_calc_offset($id, $string_stop ); seek($fh, $filestart,0); my $data; read($fh, $data, $filestop-$filestart+1); # Process quality score
$data =~ s/\n//g; $data =~ s/\r//g; my $subqual = 0; $subqual = 1 if ( $start || $stop ); my @data; if ( $subqual || ($strand == -1) ) { @data = split / /, $data, $stop+1; my $length = scalar(@data); $start = 1 if $start < 1; $stop = $length if $stop > $length; pop @data if ($stop != $length); splice @data, 0, $start-1; @data = reverse(@data) if $strand == -1; $data = join ' ', @data; } else { @data = split / /, $data; } return\@ data; } *qual = *quality =\& subqual;
}
headerdescriptionprevnextTop
sub header {
    my ($self, $id) = @_;
    $self->throw('Need to provide a sequence ID') if not defined $id;
    my ($offset, $headerlen) = (&{$self->{unpackmeth}}($self->{offsets}{$id}))[0,4];
    $offset -= $headerlen;
    my $data;
    my $fh = $self->_fh($id) or return;
    seek($fh, $offset, 0);
    read($fh, $data, $headerlen);
    chomp $data;
    substr($data, 0, 1) = '';
    return $data;
}


#-------------------------------------------------------------
# Tied hash overrides
#
}
FETCHdescriptionprevnextTop
sub FETCH {
    return shift->subqual(@_);
}


#-------------------------------------------------------------
# Bio::Seq::PrimaryQual compatibility
#
# Usage is the same as in Bio::Seq::PrimaryQual
package Bio::Seq::PrimaryQual::Qual; use overload '""' => 'display_id'; use base qw(Bio::Root::Root Bio::Seq::PrimaryQual);
}
General documentation
DATABASE CREATION AND INDEXINGTop
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.
SEE ALSOTop
Bio::DB::IndexedBase
Bio::DB::Fasta
Bio::Seq::PrimaryQual
LIMITATIONSTop
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?).
AUTHORTop
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.
APPENDIXTop
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_idTop
 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 Bio::PrimarySeqI for methods provided by the sequence objects
returned from get_Seq_by_id() and get_PrimarySeq_stream().
Args : ID
get_PrimarySeq_streamTop
 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
Top
For simple access, the following methods are provided:
newTop
 Title   : new
Usage : my $db = Bio::DB::Qual->new( $path, %options);
Function: Initialize a new database object. When indexing a directory, files
ending in .qual,qa are indexed by default.
Returns : A new Bio::DB::Qual object
Args : A single file, or path to dir, or arrayref of files
Optional arguments: see Bio::DB::IndexedBase
qualTop
 Title   : qual, quality, subqual
Usage : # All quality scores
my @qualarr = @{$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).