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Bio::Seq::Quality(3)  User Contributed Perl Documentation Bio::Seq::Quality(3)

NAME
       Bio::Seq::Quality - Implementation of sequence with residue quality
			   and trace values

SYNOPSIS
	 use Bio::Seq::Quality;

	 # input can be	space delimited	string or array	ref
	 my $qual = '0 1 2 3 4 5 6 7 8 9 11 12';
	 my $trace = '0	5 10 15	20 25 30 35 40 45 50 55';

	 my $seq = Bio::Seq::Quality->new
	     ( -qual =>	$qual,
	       -trace_indices => $trace,
	       -seq =>	'atcgatcgatcg',
	       -id  => 'human_id',
	       -accession_number => 'S000012',
	       -verbose	=> -1	# to silence deprecated	methods
	 );

	 my $quals = $seq->qual; # array ref
	 my $traces = $seq->trace;  # array ref

	 my $quals = $seq->qual_text; #	string
	 my $traces = $seq->trace_text;	# string

	 # get sub values
	 $quals	= $seq->subqual(2, 3);	# array	ref
	 $traces = $seq->subtrace(2, 3); # array ref
	 $quals	= $seq->subqual_text(2,	3); # string
	 $quals	= $seq->subtrace_text(2, 3); # string

	 # set sub values
	 $seq->subqual(2, 3, "9	9");
	 $seq->subtrace(2, 3, "9 9");

DESCRIPTION
       This object stores base quality values together with the	sequence
       string.

       The implementation is based on Bio::Seq::Meta::Array. qual() and
       trace() are base	methods	to store and retrieve information that have
       extensions to retrieve values as	a scalar (e.g. qual_text() ), or get
       or set subvalues	(e.g. subqual()	). See Bio::Seq::MetaI for more
       details.

       All the functional code is in Bio::Seq::Meta::Array.

       There deprecated	methods	that are included for compatibility with
       Bio::Seq::SeqWithQuality. These will print a warning unless verbosity
       of the object is	set to be less than zero.

SEE ALSO
       Bio::Seq::MetaI,	Bio::Seq::Meta::Array

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 - Heikki	Lehvaslaiho
       Email heikki-at-bioperl-dot-org

CONTRIBUTORS
       Chad Matsalla, bioinformatics at	dieselwurks dot	com

       Dan Bolser, dan dot bolser at gmail dot com

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

   new
	Title	: new
	Usage	: $metaseq = Bio::Seq::Quality->new
		       ( -qual => '0 1 2 3 4 5 6 7 8 9 11 12',
			 -trace	=> '0 5	10 15 20 25 30 35 40 45	50 55',
			 -seq =>  'atcgatcgatcg',
			 -id  => 'human_id',
			 -accession_number => 'S000012',
		       );
	Function: Constructor for Bio::Seq::Quality class.  Note that you can
		  provide an empty quality and trace strings.

	Returns	: a new	Bio::Seq::Quality object

   qual
	Title	: qual
	Usage	: $qual_values	= $obj->qual($values_string);
	Function:

		  Get and set method for the meta data starting	from residue
		  position one.	Since it is dependent on the length of the
		  sequence, it needs to	be manipulated after the sequence.

		  The length of	the returned value always matches the length
		  of the sequence.

	Returns	: reference to an array	of meta	data
	Args	: new value, string or array ref or Bio::Seq::PrimaryQual, optional

       Setting quality values resets the clear range.

   qual_text
	Title	: qual_text
	Usage	: $qual_values	= $obj->qual_text($values_arrayref);
	Function: Variant of meta() and	qual()	guarantied to return a string
		  representation  of meta data.	For details, see L<meta>.
	Returns	: a string
	Args	: new value, optional

   subqual
	Title	: subqual
	Usage	: $subset_of_qual_values = $obj->subqual(10, 20, $value_string);
		  $subset_of_qual_values = $obj->subqual(10, undef, $value_string);
	Function:

		  Get and set method for meta data for subsequences.

		  Numbering starts from	1 and the number is inclusive, ie 1-2
		  are the first	two residue of the sequence. Start cannot be
		  larger than end but can be equal.

		  If the second	argument is missing the	returned values
		  should extend	to the end of the sequence.

	Returns	: A reference to an array
	Args	: integer, start position
		  integer, end position, optional when a third argument	present
		  new value, optional

   subqual_text
	Title	: subqual_text
	Usage	: $meta_values	= $obj->subqual_text(20, $value_string);
	Function: Variant of subqual() returning a stringified
		  representation  of meta data.	For details, see L<Bio::Seq::MetaI>.
	Returns	: a string
	Args	: new value, optional

   quality_length
	Title	: quality_length()
	Usage	: $qual_len  = $obj->quality_length();
	Function: return the number of elements	in the quality array
	Returns	: integer
	Args	: -

   quality_is_flush
	Title	: quality_is_flush
	Usage	: $quality_is_flush  = $obj->quality_is_flush()
	Function: Boolean to tell if the trace length equals the sequence length.
		  Returns true if force_flush()	is set.
	Returns	: boolean 1 or 0
	Args	: none

   trace
	Title	: trace
	Usage	: $trace_values	 = $obj->trace($values_string);
	Function:

		  Get and set method for the meta data starting	from residue
		  position one.	Since it is dependent on the length of the
		  sequence, it needs to	be manipulated after the sequence.

		  The length of	the returned value always matches the length
		  of the sequence.

	Returns	: reference to an array	of meta	data
	Args	: new value, string or array ref, optional

   trace_text
	Title	: trace_text
	Usage	: $trace_values	 = $obj->trace_text($values_arrayref);
	Function: Variant of meta() and	trace()	 guarantied to return a	string
		  representation  of meta data.	For details, see L<meta>.
	Returns	: a string
	Args	: new value, optional

   subtrace
	Title	: subtrace
	Usage	: $subset_of_trace_values = $obj->subtrace(10, 20, $value_string);
		  $subset_of_trace_values = $obj->subtrace(10, undef, $value_string);
	Function:

		  Get and set method for meta data for subsequences.

		  Numbering starts from	1 and the number is inclusive, ie 1-2
		  are the first	two residue of the sequence. Start cannot be
		  larger than end but can be equal.

		  If the second	argument is missing the	returned values
		  should extend	to the end of the sequence.

	Returns	: A reference to an array
	Args	: integer, start position
		  integer, end position, optional when a third argument	present
		  new value, optional

   subtrace_text
	Title	: subtrace_text
	Usage	: $meta_values	= $obj->subtrace_text(20, $value_string);
	Function: Variant of subtrace()	returning a stringified
		  representation  of meta data.	For details, see L<Bio::Seq::MetaI>.
	Returns	: a string
	Args	: new value, optional

   trace_length
	Title	: trace_length()
	Usage	: $trace_len  =	$obj->trace_length();
	Function: return the number of elements	in the trace set
	Returns	: integer
	Args	: -

   trace_is_flush
	Title	: trace_is_flush
	Usage	: $trace_is_flush  = $obj->trace_is_flush()
	Function: Boolean to tell if the trace length equals the sequence length.
		  Returns true if force_flush()	is set.
	Returns	: boolean 1 or 0
	Args	: none

   get_trace_graph
	Title	 : get_trace_graph
	Usage	 : @trace_values = $obj->get_trace_graph( -trace => 'a',
							  -scale => 100)
	Function : Returns array of raw	trace values for a trace file, or
		   false if no trace data exists.  Requires a value for	trace
		   to get either the a,	g, c or	t trace	information, and an
		   optional value for scale, which rescales the	data between
		   0 and the provided value, a scale value of '0' performs no
		   scaling
	Returns	 : Array or 0
	Args	 : string, trace to retrieve, one of a,	g, c or	t integer,
		   scale, for scaling of trace between 0 and scale, or 0 for
		   no scaling, optional

   threshold
	 Title	 : threshold
	 Usage	 : $qual->threshold($value);
	 Function: Sets	the quality threshold.
	 Returns : an integer
	 Args	 : new value, optional

       Value used by *clear_range* method below.

   mask_below_threshold
	 Title	 : mask_below_threshold
	 Usage	 : $count = $obj->count_clear_ranges($threshold);
	 Function: Counts number of ranges in the sequence where quality
		   values are above the	threshold
	 Returns : count integer
	 Args	 : threshold integer, optional

       Set threshold first using method	threshold.

   count_clear_ranges
	 Title	 : count_clear_ranges
	 Usage	 : $count = $obj->count_clear_ranges($threshold);
	 Function: Counts number of ranges in the sequence where quality
		   values are above the	threshold
	 Returns : count integer
	 Args	 : threshold integer, optional

       Set threshold first using method	threshold.

   clear_ranges_length
	 Title	 : clear_ranges_length
	 Usage	 : $total_lenght = $obj->clear_ranges_length($threshold);
	 Function: Return number of residues with quality values above
		   the threshold in all	clear ranges
	 Returns : an integer
	 Args	 : threshold, optional

       Set threshold first using method	threshold.

       I think this method needs a better name!	count_high_quality_bases? or
       sum_clear_ranges?

   get_clear_range
	 Title	 : get_clear_range
	 Usage	 : $newqualobj = $obj->get_clear_range($threshold);
	 Function: Return longest subsequence that has quality values above
		   the given threshold,	or a default value of 13
	 Returns : a new Bio::Seq::Quality object
	 Args	 : threshold, optional

       Set threshold first using method	threshold.

       Note, this method could be implemented using some gaussian smoothing of
       the quality scores. Currently one base below the	threshold is enough to
       end the clear range.

   get_all_clean_ranges
	 Title	 : get_all_clean_ranges
	 Usage	 : @ranges = $obj->get_all_clean_ranges($minlength);
	 Function: Return all ranges where quality values are above
		   the threshold. Original ordering.
	 Returns : an ordered array of new Bio::Seq::Quality objects
	 Args	 : minimum length , optional

       Set threshold first using method	threshold.

perl v5.32.0			  2019-12-07		  Bio::Seq::Quality(3)

NAME | SYNOPSIS | DESCRIPTION | SEE ALSO | FEEDBACK | AUTHOR - Heikki Lehvaslaiho | CONTRIBUTORS | APPENDIX

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