/ 
bioperl-1.0.2
/ Bio::Seq::PrimaryQual

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

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

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.

quiet($mode)

Title   : quiet($mode)
Usage   : $obj->quiet(1);
Function: Shuit off warnings. Used pretty much exclusively so that make
       test doesn't spill out warnings. I wouldn't advise you turn these off
       because they are there for your own good.
Returns : Nothing
Args    : "1" for supression of warnings, "0" for normal mode.