Bio::Seq::PrimaryQual.3pm

Langue: en

Autres versions - même langue

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

Sommaire

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: 
   http://bugzilla.open-bio.org/

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.

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.