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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.

       It is a reimplementation of Chad Matsalla's Bio::Seq::SeqWithQuality
       module using Bio::Seq::MetaI.

       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.

   Differences from Bio::Seq::SeqWithQuality
       It is not possible to fully follow the interface of
       Bio::Seq::SeqWithQuality since internally a Bio::Seq::SeqWithQuality
       object is a composite of two independent objects: a Bio::PrimarySeq
       object and Bio::Seq::PrimaryQual object. Both of these objects can be
       created separately and merged into Bio::Seq::SeqWithQuality.

       This implementation is based on Bio::Seq::Meta::Array that is a
       subclass of Bio::PrimarySeq that stores any number of meta information
       in unnamed arrays.

       Here we assume that two meta sets, called 'qual' and 'trace_indices'
       are attached to a sequence. (But there is nothing that prevents you to
       add as many named meta sets as you need using normal meta() methods).

       qual() is an alias to meta(), qualat($loc) is an alias to
       submeta($loc,$loc).

       trace_indices() in Bio::Seq::SeqWithQuality has been abbreviated to
       trace() and is an alias to named_meta('trace').

       You can create an object without passing any arguments to the
       constructor (Bio::Seq::SeqWithQuality fails without alphabet). It will
       warn about not being able to set alphabet unless you set verbosity of
       the object to a negative value.

       After the latest rewrite, the meta information sets (quality and trace)
       no longer cover all the residues automatically. Methods to check the
       length of meta information (quality_length, trace_length)and to see if
       the ends are flushed to the sequence have been added (quality_is_flush,
       trace_is_flush). To force the old functinality, set force_flush to
       true.

       qual_obj() and seq_obj() methods do not exist!

       Finally, there is only one set of descriptors (primary_id, display_id,
       accession_number) for the object.

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:

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

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 cached good quality ranges that
       depend on the set threshold value.

   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 threshold for good quality values.
	 Returns : an integer
	 Args	 : new value, optional

       Value used by *clear_range* method below.

   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.

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

       Set threshold first using method threshold.

   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 v5.14.1			  2011-07-22		  Bio::Seq::Quality(3)
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