Bio::Seq Quality
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Summary
Bio::Seq::Quality - Implementation of sequence with residue quality
and trace values
Package variables
No package variables defined.
Inherit
Bio::Seq::Meta::Array
Synopsis
  use Bio::Seq::Quality;
# input can be space delimited string or array ref my $qual = '0 1 2 3 4 5 6 7 8 9 11 12'; my $trace = '0 5 10 15 20 25 30 35 40 45 50 55'; my $seq = Bio::Seq::Quality->new ( -qual => $qual, -trace_indices => $trace, -seq => 'atcgatcgatcg', -id => 'human_id', -accession_number => 'S000012', -verbose => -1 # to silence deprecated methods ); my $quals = $seq->qual; # array ref my $traces = $seq->trace; # array ref my $quals = $seq->qual_text; # string my $traces = $seq->trace_text; # string # get sub values $quals = $seq->subqual(2, 3); # array ref $traces = $seq->subtrace(2, 3); # array ref $quals = $seq->subqual_text(2, 3); # string $quals = $seq->subtrace_text(2, 3); # string # set sub values $seq->subqual(2, 3, "9 9"); $seq->subtrace(2, 3, "9 9");
Description
This object stores base quality values together with the sequence
string.
It is a reimplementation of Chad Matsalla's Bio::Seq::SeqWithQuality
module using Bio::Seq::MetaI.
The implementation is based on Bio::Seq::Meta::Array. qual() and
trace() are base methods to store and retrieve information that have
extensions to retrieve values as a scalar (e.g. qual_text() ), or get
or set subvalues (e.g. subqual() ). See Bio::Seq::MetaI for more
details.
All the functional code is in Bio::Seq::Meta::Array.
There deprecated methods that are included for compatibility with
Bio::Seq::SeqWithQuality. These will print a warning unless verbosity
of the object is set to be less than zero. It is not possible to fully follow the interface of
Bio::Seq::SeqWithQuality since internally a Bio::Seq::SeqWithQuality
object is a composite of two independent objects: a Bio::PrimarySeq
object and Bio::Seq::PrimaryQual object. Both of these objects can be
created separately and merged into Bio::Seq::SeqWithQuality.
This implementation is based on Bio::Seq::Meta::Array that is a
subclass of Bio::PrimarySeq that stores any number of meta information
in unnamed arrays.
Here we assume that two meta sets, called 'qual' and 'trace_indices'
are attached to a sequence. (But there is nothing that prevents you to
add as many named meta sets as you need using normal meta() methods).
qual() is an alias to meta(), qualat($loc) is an alias to
submeta($loc,$loc).
trace_indices() in Bio::Seq::SeqWithQuality has been abbreviated to
trace() and is an alias to named_meta('trace').
You can create an object without passing any arguments to the
constructor (Bio::Seq::SeqWithQuality fails without alphabet). It will
warn about not being able to set alphabet unless you set verbosity of
the object to a negative value.
After the latest rewrite, the meta information sets (quality and
trace) no longer cover all the residues automatically. Methods to
check the length of meta information (quality_length,
trace_length)and to see if the ends are flushed to the sequence
have been added (quality_is_flush, trace_is_flush). To force the
old functinality, set force_flush to true.
qual_obj() and seq_obj() methods do not exist!
Finally, there is only one set of descriptors (primary_id, display_id,
accession_number) for the object.
Methods
newDescriptionCode
qualDescriptionCode
qual_textDescriptionCode
subqualDescriptionCode
subqual_textDescriptionCode
quality_lengthDescriptionCode
quality_is_flushDescriptionCode
traceDescriptionCode
trace_textDescriptionCode
subtraceDescriptionCode
subtrace_textDescriptionCode
trace_lengthDescriptionCode
trace_is_flushDescriptionCode
get_trace_graphDescriptionCode
thresholdDescriptionCode
mask_below_thresholdDescriptionCode
count_clear_rangesDescriptionCode
clear_ranges_lengthDescriptionCode
get_clear_rangeDescriptionCode
get_all_clean_rangesDescriptionCode
_find_clear_ranges
No description
Code
_empty_cache
No description
Code
trace_indices
No description
Code
trace_index_at
No description
Code
sub_trace_index
No description
Code
qualat
No description
Code
baseat
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : $metaseq = Bio::Seq::Quality->new
( -qual => '0 1 2 3 4 5 6 7 8 9 11 12',
-trace => '0 5 10 15 20 25 30 35 40 45 50 55',
-seq => 'atcgatcgatcg',
-id => 'human_id',
-accession_number => 'S000012',
);
Function: Constructor for Bio::Seq::Quality class. Note that you can
provide an empty quality and trace strings.
Returns : a new Bio::Seq::Quality object
qualcodeprevnextTop
 Title   : qual
Usage : $qual_values = $obj->qual($values_string);
Function:
Get and set method for the meta data starting from residue position one. Since it is dependent on the length of the sequence, it needs to be manipulated after the sequence. The length of the returned value always matches the length of the sequence. Returns : reference to an array of meta data Args : new value, string or array ref or Bio::Seq::PrimaryQual, optional
Setting quality values resets the clear range.
qual_textcodeprevnextTop
 Title   : qual_text
Usage : $qual_values = $obj->qual_text($values_arrayref);
Function: Variant of meta() and qual() guarantied to return a string
representation of meta data. For details, see meta.
Returns : a string
Args : new value, optional
subqualcodeprevnextTop
 Title   : subqual
Usage : $subset_of_qual_values = $obj->subqual(10, 20, $value_string);
$subset_of_qual_values = $obj->subqual(10, undef, $value_string);
Function:
Get and set method for meta data for subsequences. Numbering starts from 1 and the number is inclusive, ie 1-2 are the first two residue of the sequence. Start cannot be larger than end but can be equal. If the second argument is missing the returned values should extend to the end of the sequence. Returns : A reference to an array Args : integer, start position integer, end position, optional when a third argument present new value, optional
subqual_textcodeprevnextTop
 Title   : subqual_text
Usage : $meta_values = $obj->subqual_text(20, $value_string);
Function: Variant of subqual() returning a stringified
representation of meta data. For details, see Bio::Seq::MetaI.
Returns : a string
Args : new value, optional
quality_lengthcodeprevnextTop
 Title   : quality_length()
Usage : $qual_len = $obj->quality_length();
Function: return the number of elements in the quality array
Returns : integer
Args : -
quality_is_flushcodeprevnextTop
 Title   : quality_is_flush
Usage : $quality_is_flush = $obj->quality_is_flush()
Function: Boolean to tell if the trace length equals the sequence length.
Returns true if force_flush() is set.
Returns : boolean 1 or 0
Args : none
tracecodeprevnextTop
 Title   : trace
Usage : $trace_values = $obj->trace($values_string);
Function:
Get and set method for the meta data starting from residue position one. Since it is dependent on the length of the sequence, it needs to be manipulated after the sequence. The length of the returned value always matches the length of the sequence. Returns : reference to an array of meta data Args : new value, string or array ref, optional
trace_textcodeprevnextTop
 Title   : trace_text
Usage : $trace_values = $obj->trace_text($values_arrayref);
Function: Variant of meta() and trace() guarantied to return a string
representation of meta data. For details, see meta.
Returns : a string
Args : new value, optional
subtracecodeprevnextTop
 Title   : subtrace
Usage : $subset_of_trace_values = $obj->subtrace(10, 20, $value_string);
$subset_of_trace_values = $obj->subtrace(10, undef, $value_string);
Function:
Get and set method for meta data for subsequences. Numbering starts from 1 and the number is inclusive, ie 1-2 are the first two residue of the sequence. Start cannot be larger than end but can be equal. If the second argument is missing the returned values should extend to the end of the sequence. Returns : A reference to an array Args : integer, start position integer, end position, optional when a third argument present new value, optional
subtrace_textcodeprevnextTop
 Title   : subtrace_text
Usage : $meta_values = $obj->subtrace_text(20, $value_string);
Function: Variant of subtrace() returning a stringified
representation of meta data. For details, see Bio::Seq::MetaI.
Returns : a string
Args : new value, optional
trace_lengthcodeprevnextTop
 Title   : trace_length()
Usage : $trace_len = $obj->trace_length();
Function: return the number of elements in the trace set
Returns : integer
Args : -
trace_is_flushcodeprevnextTop
 Title   : trace_is_flush
Usage : $trace_is_flush = $obj->trace_is_flush()
Function: Boolean to tell if the trace length equals the sequence length.
Returns true if force_flush() is set.
Returns : boolean 1 or 0
Args : none
get_trace_graphcodeprevnextTop
 Title    : get_trace_graph
Usage : @trace_values = $obj->get_trace_graph( -trace => 'a',
-scale => 100)
Function : Returns array of raw trace values for a trace file, or
false if no trace data exists. Requires a value for trace
to get either the a, g, c or t trace information, and an
optional value for scale, which rescales the data between
0 and the provided value, a scale value of '0' performs no
scaling
Returns : Array or 0
Args : string, trace to retrieve, one of a, g, c or t integer,
scale, for scaling of trace between 0 and scale, or 0 for
no scaling, optional
thresholdcodeprevnextTop
  Title   : threshold
Usage : $qual->threshold($value);
Function: Sets the quality threshold.
Returns : an integer
Args : new value, optional
Value used by *clear_range* method below.
mask_below_thresholdcodeprevnextTop
  Title   : mask_below_threshold
Usage : $count = $obj->count_clear_ranges($threshold);
Function: Counts number of ranges in the sequence where quality
values are above the threshold
Returns : count integer
Args : threshold integer, optional
Set threshold first using method threshold.
count_clear_rangescodeprevnextTop
  Title   : count_clear_ranges
Usage : $count = $obj->count_clear_ranges($threshold);
Function: Counts number of ranges in the sequence where quality
values are above the threshold
Returns : count integer
Args : threshold integer, optional
Set threshold first using method threshold.
clear_ranges_lengthcodeprevnextTop
  Title   : clear_ranges_length
Usage : $total_lenght = $obj->clear_ranges_length($threshold);
Function: Return number of residues with quality values above
the threshold in all clear ranges
Returns : an integer
Args : threshold, optional
Set threshold first using method threshold.
I think this method needs a better name! count_high_quality_bases? or
sum_clear_ranges?
get_clear_rangecodeprevnextTop
  Title   : get_clear_range
Usage : $newqualobj = $obj->get_clear_range($threshold);
Function: Return longest subsequence that has quality values above
the given threshold, or a default value of 13
Returns : a new Bio::Seq::Quality object
Args : threshold, optional
Set threshold first using method threshold.
Note, this method could be implemented using some gaussian smoothing
of the quality scores. Currently one base below the threshold is
enough to end the clear range.
get_all_clean_rangescodeprevnextTop
  Title   : get_all_clean_ranges
Usage : @ranges = $obj->get_all_clean_ranges($minlength);
Function: Return all ranges where quality values are above
the threshold. Original ordering.
Returns : an ordered array of new Bio::Seq::Quality objects
Args : minimum length , optional
Set threshold first using method threshold.
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;

    my $self = $class->SUPER::new(@args);

    my($meta, $qual, $trace, $trace_indices, $trace_data) =
        $self->_rearrange([qw(META
                              QUAL
                              TRACE
                              TRACE_INDICES
                              TRACE_DATA)],
                          @args);

    $self->{'_meta'}->{$DEFAULT_NAME} = [];
    $self->{'_meta'}->{'trace'} = [];
    $self->{trace_data} = $trace_data;

    $meta && $self->meta($meta);
    $qual && $self->qual($qual);
    $trace && $self->named_meta('trace', $trace);
    $trace_indices && $self->named_meta('trace', $trace_indices);

    return $self;
}



## QUAL
}
qualdescriptionprevnextTop
sub qual {
    my $self = shift;
    my $value = shift;
    $value = $value->qual
        if ref($value) and ref($value) ne 'ARRAY' and
           $value->isa('Bio::Seq::PrimaryQual');
    $self->_empty_cache if $value;
    return $self->named_meta($DEFAULT_NAME, $value);
}
qual_textdescriptionprevnextTop
sub qual_text {
    return join ' ', @{shift->named_submeta($DEFAULT_NAME, @_)};
}
subqualdescriptionprevnextTop
sub subqual {
    shift->named_submeta($DEFAULT_NAME, @_);
}
subqual_textdescriptionprevnextTop
sub subqual_text {
    return join ' ', @{shift->named_submeta($DEFAULT_NAME, @_)};
}
quality_lengthdescriptionprevnextTop
sub quality_length {
   my ($self) = @_;
   return $self->named_meta_length($DEFAULT_NAME);
}
quality_is_flushdescriptionprevnextTop
sub quality_is_flush {
    return shift->is_flush('quality');
}



## TRACE
}
tracedescriptionprevnextTop
sub trace {
    my $self = shift;
    my $value = shift;
    return $self->named_meta('trace', $value);
}
trace_textdescriptionprevnextTop
sub trace_text {
    return join ' ', @{shift->named_submeta('trace', @_)};
}
subtracedescriptionprevnextTop
sub subtrace {
    return shift->named_submeta('trace', @_);
}
subtrace_textdescriptionprevnextTop
sub subtrace_text {
    return join ' ', @{shift->named_submeta('trace', @_)};
}
trace_lengthdescriptionprevnextTop
sub trace_length {
   my ($self) = @_;
   return $self->named_meta_length('trace');
}
trace_is_flushdescriptionprevnextTop
sub trace_is_flush {
    return shift->is_flush('trace');
}
get_trace_graphdescriptionprevnextTop
sub get_trace_graph {
	my $self = shift;
        my($trace, $scale) =
	$self->_rearrange([qw(TRACE
			      SCALE
			      )],
			  @_);
	unless (defined($self->{trace_data})) { return 0 }
	unless (grep { lc($trace) eq $_ } ('a', 'g', 'c', 't')) { return 0 }
	$trace = lc($trace) . "_trace";
	my @trace_data = exists $self->{trace_data}->{$trace} &&
	    ref $self->{trace_data}->{$trace} eq 'ARRAY' ?
	    @{$self->{trace_data}->{$trace}} : ();
	my $max = $self->{trace_data}->{max_height};
	if (defined($scale) and $scale != 0)
	{
	    @trace_data = map { $_ / $max * $scale } @trace_data;
} return @trace_data;
}
thresholddescriptionprevnextTop
sub threshold {
    my $self = shift;
    my $value = shift;
    if (defined $value) {
	$self->throw("Threshold needs to be an integer [$value]")
	    unless $value =~ /^[-+]?\d+$/;
	$self->_empty_cache 
	    if defined $self->{_threshold} and $self->{_threshold} ne $value;
	$self->{_threshold} = $value;
    }
    return $self->{_threshold};
}
mask_below_thresholddescriptionprevnextTop
sub mask_below_threshold {
    my $self = shift;
    my $threshold = shift;

    $self->threshold($threshold) if defined $threshold;

    # populate the cache if needed
$self->_find_clear_ranges unless defined $self->{_ranges}; my $maskSeq = $self->seq; my $maskQual = $self->qual; ## There must be a more efficient way than this!
for(my $i=0; $i<length($maskSeq); $i++){ #print join ("\t", $i, $maskQual->[$i]), "\n";
substr($maskSeq, $i, 1, $MASK_CHAR) if $maskQual->[$i] < $self->{_threshold}; } ## This is the *wrong* way to do it!
#for my $r (@{$self->{_ranges}} ){
# substr($maskSeq, $r->{start}, $r->{length}, $MASK_CHAR x $r->{length});
#}
return $maskSeq;
}
count_clear_rangesdescriptionprevnextTop
sub count_clear_ranges {
    my $self = shift;
    my $threshold = shift;
    $self->threshold($threshold) if defined $threshold;

    # populate the cache if needed
$self->_find_clear_ranges unless defined $self->{_ranges}; return scalar @{$self->{_ranges}};
}
clear_ranges_lengthdescriptionprevnextTop
sub clear_ranges_length {
    my $self = shift;
    my $threshold = shift;
    $self->threshold($threshold) if defined $threshold;

    # populate the cache if needed
$self->_find_clear_ranges unless defined $self->{_ranges}; my $sum; map {$sum += $_->{length}} @{$self->{_ranges}}; return $sum;
}
get_clear_rangedescriptionprevnextTop
sub get_clear_range {
    my $self = shift;
    my $threshold = shift;
    $self->threshold($threshold) if defined $threshold;

    # populate the cache if needed
$self->_find_clear_ranges unless defined $self->{_ranges}; # fix for bug 2847
return unless defined $self->{_ranges}; # pick the longest
for (sort {$b->{length} <=> $a->{length} } @{$self->{_ranges}} ){ my $newqualobj = Bio::Seq::Quality->new( -seq => $self->subseq( $_->{start}, $_->{end}), -qual => $self->subqual($_->{start}, $_->{end}), -id => $self->id); $newqualobj->threshold($threshold); return $newqualobj; }
}
get_all_clean_rangesdescriptionprevnextTop
sub get_all_clean_ranges {
    my $self = shift;
    my $minl = shift || 0;

    $self->throw("Mimimum length needs to be zero or a positive integer [$minl]")
        unless $minl =~ /^\+?\d+$/;

    # populate the cache if needed
$self->_find_clear_ranges unless defined $self->{_ranges}; # return in the order of occurrence
my @ranges; for my $r (sort {$b->{start} <=> $a->{start} } @{$self->{_ranges}} ){ next if $r->{length} < $minl; ## Constructor should allow "-threshold => ..."!
push @ranges, Bio::Seq::Quality->new ( -seq => $self->subseq( $r->{start}, $r->{end}), -qual => $self->subqual($r->{start}, $r->{end}), -id => $self->id ); } return @ranges; } #
# _find_clear_ranges: where range/threshold calculations happen
#
}
_find_clear_rangesdescriptionprevnextTop
sub _find_clear_ranges {
    my $self = shift;
    my $qual = $self->qual;
    
    $self->throw("You need to set the threshold value first")
        unless defined $self->threshold;
    
    my $threshold = $self->threshold;
    
    my $rangeFlag = 0;
    
    for(my $i=0; $i<@$qual; $i++){
	## Are we currently within a clear range or not?
if($rangeFlag){ ## Did we just leave the clear range?
if($qual->[$i]<$threshold){ ## Log the range
my $range; $range->{end} = $i-1; $range->{start} = $rangeFlag; $range->{length} = $i - $rangeFlag; push @{$self->{_ranges}}, $range; ## and reset the range flag.
$rangeFlag = 0; } ## else nothing changes
} else{ ## Did we just enter a clear range?
if($qual->[$i]>=$threshold){ ## then set the range flag!
$rangeFlag = $i; } ## else nothing changes
} } ## Did we exit the last clear range?
if($rangeFlag){ my $i = scalar(@$qual); ## Log the range
my $range; $range->{end} = $i-1; $range->{start} = $rangeFlag; $range->{length} = $i - $rangeFlag; push @{$self->{_ranges}}, $range; } 1;
}
_empty_cachedescriptionprevnextTop
sub _empty_cache {
    my $self = shift;
    undef $self->{_ranges};
}




################## deprecated methods ##################
}
trace_indicesdescriptionprevnextTop
sub trace_indices {
    my $self = shift;
    return $self->named_meta('trace');
}
trace_index_atdescriptionprevnextTop
sub trace_index_at {
    my ($self, $val) =@_;
    return shift @{$self->named_submeta('trace', $val, $val)};
}
sub_trace_indexdescriptionprevnextTop
sub sub_trace_index {
    my $self = shift; 
    return $self->named_submeta('trace', @_);
}
qualatdescriptionprevnextTop
sub qualat {
    my ($self, $val) =@_;
    return shift @{$self->submeta($val, $val)};
}
baseatdescriptionprevnextTop
sub baseat {
    my ($self,$val) = @_;
    return $self->subseq($val,$val);
}



1;
}
General documentation
SEE ALSOTop
Bio::Seq::MetaI,
Bio::Seq::Meta::Array
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki LehvaslaihoTop
Email heikki-at-bioperl-dot-org
CONTRIBUTORSTop
Chad Matsalla, bioinformatics at dieselwurks dot com
Dan Bolser, dan dot bolser at gmail dot com
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _