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BioPerl-1.007000_005
River stage two • 60 direct dependents • 65 total dependents
/ Bio::LocatableSeq

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())