Provided by: libbio-perl-perl_1.6.923-1_all 
NAME
Bio::Seq::Quality - Implementation of sequence with residue quality
and trace values
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");
$seq->subtrace(2, 3, "9 9");
DESCRIPTION
This object stores base quality values together with the sequence string.
It is a reimplementation of Chad Matsalla's Bio::Seq::SeqWithQuality module using
Bio::Seq::MetaI.
The implementation is based on Bio::Seq::Meta::Array. qual() and trace() are base methods
to store and retrieve information that have extensions to retrieve values as a scalar
(e.g. qual_text() ), or get or set subvalues (e.g. subqual() ). See Bio::Seq::MetaI for
more details.
All the functional code is in Bio::Seq::Meta::Array.
There deprecated methods that are included for compatibility with
Bio::Seq::SeqWithQuality. These will print a warning unless verbosity of the object is set
to be less than zero.
Differences from Bio::Seq::SeqWithQuality
It is not possible to fully follow the interface of Bio::Seq::SeqWithQuality since
internally a Bio::Seq::SeqWithQuality object is a composite of two independent objects: a
Bio::PrimarySeq object and Bio::Seq::PrimaryQual object. Both of these objects can be
created separately and merged into Bio::Seq::SeqWithQuality.
This implementation is based on Bio::Seq::Meta::Array that is a subclass of
Bio::PrimarySeq that stores any number of meta information in unnamed arrays.
Here we assume that two meta sets, called 'qual' and 'trace_indices' are attached to a
sequence. (But there is nothing that prevents you to add as many named meta sets as you
need using normal meta() methods).
qual() is an alias to meta(), qualat($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.
SEE ALSO
Bio::Seq::MetaI, Bio::Seq::Meta::Array
FEEDBACK
Mailing Lists
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
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 Bugs
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 Lehvaslaiho
Email heikki-at-bioperl-dot-org
CONTRIBUTORS
Chad Matsalla, bioinformatics at dieselwurks dot com
Dan Bolser, dan dot bolser at gmail dot com
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are
usually preceded with a _
new
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
qual
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_text
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 L<meta>.
Returns : a string
Args : new value, optional
subqual
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_text
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 L<Bio::Seq::MetaI>.
Returns : a string
Args : new value, optional
quality_length
Title : quality_length()
Usage : $qual_len = $obj->quality_length();
Function: return the number of elements in the quality array
Returns : integer
Args : -
quality_is_flush
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
trace
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_text
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 L<meta>.
Returns : a string
Args : new value, optional
subtrace
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_text
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 L<Bio::Seq::MetaI>.
Returns : a string
Args : new value, optional
trace_length
Title : trace_length()
Usage : $trace_len = $obj->trace_length();
Function: return the number of elements in the trace set
Returns : integer
Args : -
trace_is_flush
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_graph
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
threshold
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_threshold
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_ranges
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_length
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_range
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_ranges
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.