Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Seq::PrimaryQual - Bioperl lightweight Quality Object


        use Bio::Seq::PrimaryQual;

        # you can use either a space-delimited string for quality

        my $string_quals = "10 20 30 40 50 40 30 20 10";
        my $qualobj = Bio::Seq::PrimaryQual->new(
            -qual             => $string_quals,
            -id               => 'QualityFragment-12',
            -accession_number => 'X78121',

        # _or_ you can use an array of quality values

        my @q2 = split/ /,$string_quals;
        $qualobj = Bio::Seq::PrimaryQual->new(
            -qual              => \@q2,
            -primary_id        => 'chads primary_id',
            -desc              => 'chads desc',
            -accession_number  => 'chads accession_number',
            -id                => 'chads id'

        # to get the quality values out:

        my @quals = @{$qualobj->qual()};

        # to give _new_ quality values

        my $newqualstring = "50 90 1000 20 12 0 0";


       This module provides a mechanism for storing quality values. Much more useful as part of
       Bio::Seq::SeqWithQuality where these quality values are associated with the sequence


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AUTHOR - Chad Matsalla



       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        Title   : new()
        Usage   : $qual = Bio::Seq::PrimaryQual->new(
                      -qual             => '10 20 30 40 50 50 20 10',
                      -id               => 'human_id',
                      -accession_number => 'AL000012',

        Function: Returns a new Bio::Seq::PrimaryQual object from basic
                  constructors, being a string _or_ a reference to an array for the
                  sequence and strings for id and accession_number. Note that you
                  can provide an empty quality string.
        Returns : a new Bio::Seq::PrimaryQual object

        Title   : qual()
        Usage   : @quality_values  = @{$obj->qual()};
        Function: Get or set the quality as a reference to an array containing the
                  quality values. An error is generated if the quality scores are
                  invalid, see validate_qual().
        Returns : A reference to an array.

        Title    : seq()
        Usager   : $sequence = $obj->seq();
        Function : Returns the quality numbers as a space-separated string.
        Returns  : Single string.
        Args     : None.

        Title   : validate_qual($qualstring)
        Usage   : print("Valid.") if { &validate_qual($self, $quality_string); }
        Function: Test that the given quality string is valid. It is expected to
                  contain space-delimited numbers that can be parsed using split /\d+/.
                  However, this validation takes shortcuts and only tests that the
                  string contains characters valid in numbers: 0-9 . eE +-
                  Note that empty quality strings are valid too.
        Returns : 1 for a valid sequence, 0 otherwise
        Args    : - Scalar containing the quality string to validate.
                  - Boolean to optionally throw an error if validation failed

        Title   : subqual($start,$end)
        Usage   : @subset_of_quality_values = @{$obj->subqual(10,40)};
        Function: returns the quality values from $start to $end, where the
                  first value is 1 and the number is inclusive, ie 1-2 are the
                  first two bases of the sequence. Start cannot be larger than
                  end but can be equal.
        Returns : A reference to an array.
        Args    : a start position and an end position

        Title   : display_id()
        Usage   : $id_string = $obj->display_id();
        Function: returns the display id, aka the common name of the Quality
                  The semantics of this is that it is the most likely string to be
                  used as an identifier of the quality sequence, and likely to have
                  "human" readability.  The id is equivalent to the ID field of the
                  GenBank/EMBL databanks and the id field of the Swissprot/sptrembl
                  database. In fasta format, the >(\S+) is presumed to be the id,
                  though some people overload the id to embed other information.
                  Bioperl does not use any embedded information in the ID field,
                  and people are encouraged to use other mechanisms (accession
                  field for example, or extending the sequence object) to solve
                  this. Notice that $seq->id() maps to this function, mainly for
                  legacy/convience issues
        Returns : A string
        Args    : None

        Title   : header()
        Usage   : $header = $obj->header();
        Function: Get/set the header that the user wants printed for this
            quality object.
        Returns : A string
        Args    : None

        Title   : accession_number()
        Usage   : $unique_biological_key = $obj->accession_number();
        Function: Returns the unique biological id for a sequence, commonly
               called the accession_number. For sequences from established
               databases, the implementors should try to use the correct
               accession number. Notice that primary_id() provides the unique id
               for the implementation, allowing multiple objects to have the same
               accession number in a particular implementation. For sequences
               with no accession number, this method should return "unknown".
        Returns : A string
        Args    : None

        Title   : primary_id()
        Usage   : $unique_implementation_key = $obj->primary_id();
        Function: Returns the unique id for this object in this implementation.
               This allows implementations to manage their own object ids in a
               way the implementation can control clients can expect one id to
               map to one object. For sequences with no accession number, this
               method should return a stringified memory location.
        Returns : A string
        Args    : None

        Title   : desc()
        Usage   : $qual->desc($newval);
                  $description = $qual->desc();
        Function: Get/set description text for a qual object
        Example :
        Returns : Value of desc
        Args    : newvalue (optional)

        Title   : id()
        Usage   : $id = $qual->id();
        Function: Return the ID of the quality. This should normally be (and
                  actually is in the implementation provided here) just a synonym
                  for display_id().
        Returns : A string.
        Args    : None.

        Title   : length()
        Usage   : $length = $qual->length();
        Function: Return the length of the array holding the quality values.
                  Under most circumstances, this should match the number of quality
                  values but no validation is done when the PrimaryQual object is
                  constructed and non-digits could be put into this array. Is this
                  a bug? Just enough rope...
        Returns : A scalar (the number of elements in the quality array).
        Args    : None.

        Title   : qualat
        Usage   : $quality = $obj->qualat(10);
        Function: Return the quality value at the given location, where the
                  first value is 1 and the number is inclusive, ie 1-2 are the first
                  two bases of the sequence. Start cannot be larger than end but can
                  be equal.
        Returns : A scalar.
        Args    : A position.

        Title   : to_string()
        Usage   : $quality = $obj->to_string();
        Function: Return a textual representation of what the object contains.
                  For this module, this function will return:
        Returns : A scalar.
        Args    : None.