man Bio::Seq::Quality (3): Implementation of sequence with residue quality

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.

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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://github.com/bioperl/bioperl-live/issues

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.