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

NAME

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

SYNOPSIS

        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";
        $qualobj->qual($newqualstring);

DESCRIPTION

       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
       information.

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 - Chad Matsalla

       Email bioinformatics@dieselwurks.com

APPENDIX

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

   new()
        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

   qual()
        Title   : qual()
        Usage   : @quality_values  = @{$obj->qual()};
        Function: Returns the quality as a reference to an array containing the
                  quality values. The individual elements of the quality array are
                  not validated and can be any numeric value.
        Returns : A reference to an array.

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

   validate_qual($qualstring)
        Title   : validate_qual($qualstring)
        Usage   : print("Valid.") if { &validate_qual($self,$qualities); }
        Function: Make sure that the quality, if it has length > 0, contains at
               least one digit. Note that quality strings are parsed into arrays
               using split/\d+/,$quality_string, so make sure that your quality
               scalar looks like this if you want it to be parsed properly.
        Returns : 1 for a valid sequence (WHY? Shouldn\'t it return 0? <boggle>)
        Args    : a scalar (any scalar, why PrimarySeq author?) and a scalar
               containing the string to validate.

   subqual($start,$end)
        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

   display_id()
        Title   : display_id()
        Usage   : $id_string = $obj->display_id();
        Function: returns the display id, aka the common name of the Quality
               object.
               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

   header()
        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

   accession_number()
        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 implemetation, 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

   primary_id()
        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 implementaiton 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

   desc()
        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)

   id()
        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.

   length()
        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.

   qualat($position)
        Title   : qualat($position)
        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.

   to_string()
        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:
                       qual
                       display_id
                       accession_number
                       primary_id
                       desc
                       id
                       length
        Returns : A scalar.
        Args    : None.