Provided by: libbio-perl-perl_1.6.901-2_all bug

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.