Christopher Fields > BioPerl-1.6.901 > Bio::Seq::PrimaryQual

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Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.924

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.
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