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Bio::Seq::PrimaryQual(User Contributed Perl DocumentatBio::Seq::PrimaryQual(3)

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://github.com/bioperl/bioperl-live/issues

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: 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.

   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, $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

   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()
	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.

   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.

perl v5.24.1			  2017-07-08	      Bio::Seq::PrimaryQual(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Chad Matsalla | APPENDIX

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