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

NAME
       Bio::Seq::Meta -	Generic	superclass for sequence	objects	with
       residue-based meta information

SYNOPSIS
	 use Bio::LocatableSeq;
	 use Bio::Seq::Meta;
	 use Bio::Tools::OddCodes;
	 use Bio::SeqIO;

	 my $seq = Bio::Seq::Meta->new(-id=>'test',
					  -seq=>'ACTGCTAGCT',
					  -start=>2434,
					  -end=>2443,
					  -strand=>1,
					  -verbose=>1, # to see	warnings
					 );

	 # the existing	sequence object	can be a Bio::PrimarySeq, too

	 # to test this	is a meta seq object
	 $seq->isa("Bio::Seq::Meta")
	     ||	$seq->throw("$seq is not a Bio::Seq::Meta");

	 $seq->meta('1234567890');
	 $seq =	Bio::Seq::Meta->new(-id=>'test',
				    -seq=>'HACILMIFGT',
				    -start=>2434,
				    -end=>2443,
				    -strand=>1,
				    -meta=>'1234567890',
				    -verbose=>1, # to see warnings
				   );

	 # accessors
	 $string     = $seq->meta_text();
	 $substring  = $seq->submeta_text(2,5);
	 $unique_key = $seq->accession_number();

	 # storing output from Bio::Tools::OddCodes as meta data
	 my $protcodes = Bio::Tools::OddCodes->new(-seq	=> $seq);
	 my @codes = qw(structural chemical functional charge hydrophobic);
	 map { $seq->named_meta($_, ${$protcodes->$_($seq) } )}	@codes;

	 my $out = Bio::SeqIO->new(-format=>'metafasta');
	 $out->write_seq($seq);

DESCRIPTION
       This class implements generic methods for sequences with	residue-based
       meta information. Meta sequences	with meta data are Bio::LocatableSeq
       objects with additional methods to store	that meta information. See
       Bio::LocatableSeq and Bio::Seq::MetaI.

       The meta	information in this class is always one	character per residue
       long and	blank values are space characters (ASCII 32).

       After the latest	rewrite, the meta information no longer	covers all the
       residues	automatically. Methods to check	the length of meta information
       (meta_length)and	to see if the ends are flushed to the sequence have
       been added (is_flush). To force the old functionality, set force_flush
       to true.

       It is assumed that meta data values do not depend on the	nucleotide
       sequence	strand value.

       Application specific implementations should inherit from	this class to
       override	and add	to these methods.

       Bio::Seq::Meta::Array allows for	more complex meta values (scalars or
       objects)	to be used.

   Method naming
       Character based meta data is read and set by method meta() and its
       variants. These are the suffixes	and prefixes used in the variants:

	   [named_] [sub] meta [_text]

       _text
	  Suffix _text guaranties that output is a string. Note	that it	does
	  not limit the	input.

	  In this implementation, the output is	always text, so	these methods
	  are redundant.

       sub
	  Prefix sub, like in subseq(),	means that the method applies to sub
	  region of the	sequence range and takes start and end as arguments.
	  Unlike subseq(), these methods are able to set values.  If the range
	  is not defined, it defaults to the complete sequence.

       named
	  Prefix named_	in method names	allows the used	to attach multiple
	  meta strings to one sequence by explicitly naming them. The name is
	  always the first argument to the method. The "unnamed" methods use
	  the class wide default name for the meta data	and are	thus special
	  cases	"named"	methods.

	  Note that internally names are keys in a hash	and any	misspelling of
	  a name will silently store the data under a wrong name. The used
	  names	(keys) can be retrieved	using method meta_names(). See
	  meta_names.

NOTE
       This Bio::Seq::MetaI implementation inherits from Bio::LocatableSeq,
       which itself inherits from Bio::PrimarySeq. It is not a Bio::SeqI, so
       bless-ing objects of this class into a Bio::SeqI	or vice	versa and will
       not work	as expected (see bug 2262). This may be	addressed in a future
       refactor	of Bio::LocatableSeq.

SEE ALSO
       Bio::LocatableSeq, 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@dieselwurks.com

       Aaron Mackey, amackey@virginia.edu

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::Meta->new
		       ( -meta => 'aaaaaaaabbbbbbbb',
			 -seq =>  'TKLMILVSHIVILSRM'
			 -id  => 'human_id',
			 -accession_number => 'S000012',
		       );
	Function: Constructor for Bio::Seq::Meta class,	meta data being	in a
		  string. Note that you	can provide an empty quality string.
	Returns	: a new	Bio::Seq::Meta object

   meta
	Title	: meta
	Usage	: $meta_values	= $obj->meta($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, if force_flush() is set. See	L<force_flush>.

	Returns	: meta data in a string
	Args	: new value, string, optional

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

   named_meta
	Title	: named_meta()
	Usage	: $meta_values	= $obj->named_meta($name, $values_arrayref);
	Function: A more general version of meta(). Each meta data set needs
		  to be	named. See also	L<meta_names>.
	Returns	: a string
	Args	: scalar, name of the meta data	set
		  new value, optional

   _test_gap_positions
	Title	: _test_gap_positions
	Usage	: $meta_values	= $obj->_test_gap_positions($name);
	Function: Internal test	for correct position of	gap characters.
		  Gap being only '-' this time.

		  This method is called	from named_meta() when setting meta
		  data but only	if verbose is positive as this can be an
		  expensive process on very long sequences. Set	verbose(1) to
		  see warnings when gaps do not	align in sequence and meta
		  data and turn	them into errors by setting verbose(2).

	Returns	: true on success, prints warnings
	Args	: none

   named_meta_text
	Title	: named_meta_text()
	Usage	: $meta_values	= $obj->named_meta_text($name, $values_arrayref);
	Function: Variant of named_meta() guarantied to	return a textual
		  representation  of the named meta data.
		  For details, see L<meta>.
	Returns	: a string
	Args	: scalar, name of the meta data	set
		  new value, optional

   submeta
	Title	: submeta
	Usage	: $subset_of_meta_values = $obj->submeta(10, 20, $value_string);
		  $subset_of_meta_values = $obj->submeta(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.

		  The return value may be a string or an array reference,
		  depending on the implementation. If in doubt,	use
		  submeta_text() which is a variant guarantied to return a
		  string.  See L<submeta_text>.

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

   submeta_text
	Title	: submeta_text
	Usage	: $meta_values	= $obj->submeta_text(20, $value_string);
	Function: Variant of submeta() guarantied to return a textual
		  representation  of meta data.	For details, see L<meta>.
	Returns	: a string
	Args	: new value, optional

   named_submeta
	Title	: named_submeta
	Usage	: $subset_of_meta_values = $obj->named_submeta($name, 10, 20, $value_string);
		  $subset_of_meta_values = $obj->named_submeta($name, 10);
	Function: Variant of submeta() guarantied to return a textual
		  representation  of meta data.	For details, see L<meta>.
	Returns	: A reference to an array or a string
	Args	: scalar, name of the meta data	set
		  integer, start position
		  integer, end position, optional when a third argument	present
		  new value, optional

   named_submeta_text
	Title	: named_submeta_text
	Usage	: $meta_values	= $obj->named_submeta_text($name, 20, $value_string);
	Function: Variant of submeta() guarantied to return a textual
		  representation  of meta data.	For details, see L<meta>.
	Returns	: a string
	Args	: scalar, name of the meta data
	Args	: integer, start position, optional
		  integer, end position, optional
		  new value, optional

   meta_names
	Title	: meta_names
	Usage	: @meta_names  = $obj->meta_names()
	Function: Retrieves an array of	meta data set names. The default
		  (unnamed) set	name is	guarantied to be the first name.
	Returns	: an array of names
	Args	: none

   meta_length
	Title	: meta_length()
	Usage	: $meeta_len  =	$obj->meta_length();
	Function: return the number of elements	in the meta set
	Returns	: integer
	Args	: -

   named_meta_length
	Title	: named_meta_length()
	Usage	: $meta_len  = $obj->named_meta_length($name);
	Function: return the number of elements	in the named meta set
	Returns	: integer
	Args	: -

   force_flush
	Title	: force_flush()
	Usage	: $force_flush = $obj->force_flush(1);
	Function: Automatically	pad with empty values or truncate meta values
		  to sequence length. Not done by default.
	Returns	: boolean 1 or 0
	Args	: optional boolean value

       Note that if you	turn this forced padding off, the previously padded
       values are not changed.

   _do_flush
	Title	: _do_flush
	Usage	:
	Function: internal method to do	the force that meta values are same
		  length as the	sequence . Called from L<force_flush>
	Returns	:
	Args	:

   is_flush
	Title	: is_flush
	Usage	: $is_flush  = $obj->is_flush()
		  or  $is_flush	= $obj->is_flush($my_meta_name)
	Function: Boolean to tell if all meta values are in
		  flush	with the sequence length.
		  Returns true if force_flush()	is set
		  Set verbosity	to a positive value to see failed meta sets
	Returns	: boolean 1 or 0
	Args	: optional name	of the meta set

Bio::PrimarySeqI methods
   revcom
	Title	: revcom
	Usage	: $newseq = $seq->revcom();
	Function: Produces a new Bio::Seq::MetaI implementing object where
		  the order of residues	and their meta information is reversed.
	Returns	: A new	(fresh)	Bio::Seq::Meta object
	Args	: none
	Throws	: if the object	returns	false on is_flush()

       Note: The method	does nothing to	meta values, it	reorders them, only.

   trunc
	Title	: trunc
	Usage	: $subseq = $seq->trunc(10,100);
	Function: Provides a truncation	of a sequence together with meta data
	Returns	: a fresh Bio::Seq::Meta implementing object
	Args	: Two integers denoting	first and last residue of the sub-sequence.

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

NAME | SYNOPSIS | DESCRIPTION | NOTE | SEE ALSO | FEEDBACK | AUTHOR - Heikki Lehvaslaiho | CONTRIBUTORS | APPENDIX | Bio::PrimarySeqI methods

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