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Bio::LocatableSeq(3)  User Contributed Perl Documentation Bio::LocatableSeq(3)

NAME
       Bio::LocatableSeq - A Bio::PrimarySeq object with start/end points on
       it that can be projected	into a MSA or have coordinates relative	to
       another seq.

SYNOPSIS
	   use Bio::LocatableSeq;
	   my $seq = Bio::LocatableSeq->new(-seq => "CAGT-GGT",
			   -id	=> "seq1",
			   -start => 1,
			   -end	  => 7);

	   # a normal sequence object
	   $locseq->seq();
	   $locseq->id();

	   # has start,end points
	   $locseq->start();
	   $locseq->end();

	   # inherits off RangeI, so range operations possible

DESCRIPTION
       The LocatableSeq	sequence object	was developed mainly because the
       SimpleAlign object requires this	functionality, and in the rewrite of
       the Sequence object we had to decide what to do with this.

       It is, to be honest, not	well integrated	with the rest of bioperl. For
       example,	the trunc() function does not return a LocatableSeq object, as
       some might have thought.	Also, the sequence is not a Bio::SeqI, so the
       location	is simply inherited from Bio::RangeI and is not	stored in a
       Bio::Location.

       There are all sorts of nasty gotcha's about interactions	between
       coordinate systems when these sort of objects are used. Some mapping
       now occurs to deal with HSP data, however it can	probably be integrated
       in better and most methods do not implement it correctly	yet. Also,
       several PrimarySeqI methods (subseq(), trunc(), etc.) do	not behave as
       expected	and must be used with care. Due	to this, LocatableSeq
       functionality is	to be refactored in a future BioPerl release.
       However,	for alignment functionality it works adequately	for the	time
       being.

       If you do not need alignment functionality,
       Bio::SeqfeatureI-implementing modules may be a suitable alternative to
       Bio::LocatableSeq. For example, Bio::SeqFeature::Generic	and
       Bio::SeqFeature::Lite provide methods to	attach a sequence to a
       specific	region of a parent sequence and	to set other useful
       attributes.

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

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

   start
	Title	: start
	Usage	: $obj->start($newval)
	Function: Get/set the 1-based start position of	this sequence in the original
		  sequence. '0'	means before the original sequence starts.
	Returns	: value	of start
	Args	: newvalue (optional)

   end
	Title	: end
	Usage	: $obj->end($newval)
	Function: Get/set the 1-based end position of this sequence in the original
		  sequence. '0'	means before the original sequence starts.
	Returns	: value	of end
	Args	: newvalue (optional)
	Note	: although this	is a get/set, it checks	passed values against the
		  calculated end point ( derived from the sequence and based on
		  $GAP_SYMBOLS and possible frameshifts() ).  If there is no match,
		  it will warn and set the proper value.  Probably best	used for
		  debugging proper sequence calculations.

   strand
	Title	: strand
	Usage	: $obj->strand($newval)
	Function: return or set	the strandedness
	Returns	: the value of the strandedness	(-1, 0 or 1)
	Args	: the value of the strandedness	(-1, 0 or 1)

   mapping
	Title	: mapping
	Usage	: $obj->mapping($newval)
	Function: return or set	the mapping indices (indicates # symbols/positions in
		  the source string mapping to # of coordinate positions)
	Returns	: two-element array (# symbols => # coordinate pos)
	Args	: two elements (# symbols => # coordinate pos);	this can also be
		  passed in as an array	reference of the two elements (as might	be
		  passed upon Bio::LocatableSeq	instantiation, for instance).

   frameshifts
	Title	: frameshifts
	Usage	: $obj->frameshifts($newval)
	Function: get/set the frameshift hash, which contains sequence positions as
		  keys and the shift (-2, -1, 1, 2) as the value
	Returns	: hash
	Args	: hash or hash reference

   get_nse
	Title	: get_nse
	Usage	:
	Function: read-only name of form id/start-end
	Example	:
	Returns	:
	Args	:

   force_nse
	Title	: force_nse
	Usage	: $ls->force_nse()
	Function: Boolean which	forces get_nse() to build an NSE, regardless
		  of whether id(), start(), or end() is	set
	Returns	: Boolean value
	Args	: (optional) Boolean (1	or 0)
	Note	: This will convert any	passed value evaluating	as TRUE/FALSE to 1/0
		  respectively

   num_gaps
	Title	: num_gaps
	Usage	:$self->num_gaps('.')
	Function:Gets number of	gaps in	the sequence. The count	excludes
		  leading or trailing gap characters.

		  Valid	bioperl	sequence characters are	[A-Za-z\-\.\*].	Of
		  these, '.' and '-' are counted as gap	characters unless an
		  optional argument specifies one of them.

	Returns	: number of internal gaps in the sequence.
	Args	: a gap	character (optional)
	Status	: Stable
	Note	: replaces no_gaps

   column_from_residue_number
	Title	: column_from_residue_number
	Usage	: $col = $seq->column_from_residue_number($resnumber)
	Function:

		  This function	gives the position in the alignment
		  (i.e.	column number) of the given residue number in the
		  sequence. For	example, for the sequence

		Seq1/91-97 AC..DEF.GH

		  column_from_residue_number(94) returns 6.

		  An exception is thrown if the	residue	number would lie
		  outside the length of	the aligment
		  (e.g.	column_from_residue_number( "Seq2", 22 )

	Returns	: A column number for the position of the
		  given	residue	in the given sequence (1 = first column)
	Args	: A residue number in the whole	sequence (not just that
		  segment of it	in the alignment)

   location_from_column
	Title	: location_from_column
	Usage	: $loc = $ali->location_from_column($column_number)
	Function:

		  This function	gives the residue number for a given position
		  in the alignment (i.e. column	number)	of the given. Gaps
		  complicate this process and force the	output to be a
		  L<Bio::Location::Simple> where values	can be undefined.
		  For example, for the sequence:

		Seq/91-96 .AC..DEF.G.

		  location_from_column(	3 ) position 92
		  location_from_column(	4 ) position 92^93
		  location_from_column(	9 ) position 95^96
		  location_from_column(	1 ) position undef

		  An exact position returns a Bio::Location::Simple object
		  where	where location_type() returns 'EXACT', if a position
		  is between bases location_type() returns 'IN-BETWEEN'.
		  Column before	the first residue returns undef. Note that if
		  the position is after	the last residue in the	alignment,
		  that there is	no guarantee that the original sequence	has
		  residues after that position.

		  An exception is thrown if the	column number is not within
		  the sequence.

	Returns	: Bio::Location::Simple	or undef
	Args	: A column number
	Throws	: If column is not within the sequence

       See Bio::Location::Simple for more.

   revcom
	Title	: revcom
	Usage	: $rev = $seq->revcom()
	Function: Produces a new Bio::LocatableSeq object which
		  has the reversed complement of the sequence. For protein
		  sequences this throws	an exception of	"Sequence is a
		  protein. Cannot revcom"

	Returns	: A new	Bio::LocatableSeq object
	Args	: none

   trunc
	Title	: trunc
	Usage	: $subseq = $myseq->trunc(10,100);
	Function: Provides a truncation	of a sequence,
	Returns	: a fresh Bio::PrimarySeqI implementing	object
	Args	: Two integers denoting	first and last columns of the
		  sequence to be included into sub-sequence.

   validate_seq
	Title	: validate_seq
	Usage	: if(! $seqobj->validate_seq($seq_str) ) {
		       print "sequence $seq_str	is not valid for an object of
		       alphabet	",$seqobj->alphabet, "\n";
		  }
	Function: Test that the	given sequence is valid, i.e. contains only valid
		  characters. The allowed characters are all letters (A-Z) and '-','.',
		  '*','?','=' and '~'. Spaces are not valid. Note that this
		  implementation does not take alphabet() into account.
	Returns	: 1 if the supplied sequence string is valid, 0	otherwise.
	Args	: - Sequence string to be validated
		  - Boolean to throw an	error if the sequence is invalid

   no_gap
	Title	  : no_gaps
	Usage	  : $self->no_gaps('.')
	Function  : Gets number	of gaps	in the sequence. The count excludes
		    leading or trailing	gap characters.

		    Valid bioperl sequence characters are [A-Za-z\-\.\*]. Of
		    these, '.' and '-' are counted as gap characters unless an
		    optional argument specifies	one of them.

	Returns	  : number of internal gaps in the sequence.
	Args	  : a gap character (optional)
	Status	  : Deprecated (in favor of num_gaps())

   no_sequences
	Title	  : no_sequences
	Usage	  : $gaps = $seq->no_sequences
	Function  : number of sequence in the sequence alignment
	Returns	  : integer
	Argument  :
	Status	  : Deprecated (in favor of num_sequences())

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | APPENDIX

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