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())