NAME

Bio::DB::GFF::Segment -- Simple DNA segment object

SYNOPSIS

See Bio::DB::GFF.

DESCRIPTION

Bio::DB::GFF::Segment provides the basic representation of a range of DNA contained in a GFF database. It is the base class from which the Bio::DB::GFF::RelSegment and Bio::DB::GFF::Feature classes are derived.

Generally, you will not create or manipulate Bio::DB::GFF::Segment objects directly, but use those that are returned by the Bio::DB::GFF module.

API

The remainder of this document describes the API for Bio::DB::GFF::Segment.

new

Title   : new
Usage   : $s = Bio::DB::GFF::Segment->new(@args)
Function: create a new segment
Returns : a new Bio::DB::GFF::Segment object
Args    : see below
Status  : Public

This method creates a new Bio::DB::GFF::Segment object. Generally this is called automatically by the Bio::DB::GFF module and derivatives.

There are five positional arguments:

$factory      a Bio::DB::GFF::Adaptor to use for database access
$sourceseq    ID of the source sequence
$sourceclass  class of the source sequence
$start        start of the desired segment relative to source sequence
$stop         stop of the desired segment relative to source sequence

factory

Title   : factory
Usage   : $s->factory
Function: get the factory object
Returns : a Bio::DB::GFF::Adaptor
Args    : none
Status  : Public

This is a read-only accessor for the Bio::DB::GFF::Adaptor object used to create the segment.

start

Title   : start
Usage   : $s->start
Function: start of segment
Returns : integer
Args    : none
Status  : Public

This is a read-only accessor for the start of the segment.

end

Title   : end
Usage   : $s->end
Function: end of segment
Returns : integer
Args    : none
Status  : Public

This is a read-only accessor for the end of the segment.

stop

Title   : stop
Usage   : $s->stop
Function: stop of segment
Returns : integer
Args    : none
Status  : Public

This is an alias for end(), provided for AcePerl compatibility.

length

Title   : length
Usage   : $s->length
Function: length of segment
Returns : integer
Args    : none
Status  : Public

Returns the length of the segment. Always a positive number.

strand

Title   : strand
Usage   : $s->strand
Function: strand of segment
Returns : +1,0,-1
Args    : none
Status  : Public

Returns the strand on which the segment resides, either +1, 0 or -1.

low

Title   : low
Usage   : $s->low
Function: return lower coordinate
Returns : lower coordinate
Args    : none
Status  : Public

Returns the lower coordinate, either start or end.

high

Title   : high
Usage   : $s->high
Function: return higher coordinate
Returns : higher coordinate
Args    : none
Status  : Public

Returns the higher coordinate, either start or end.

sourceseq

Title   : sourceseq
Usage   : $s->sourceseq
Function: get the segment source
Returns : a string
Args    : none
Status  : Public

Returns the name of the source sequence for this segment.

class

Title   : class
Usage   : $s->class([$newclass])
Function: get the source sequence class
Returns : a string
Args    : new class (optional)
Status  : Public

Gets or sets the class for the source sequence for this segment.

subseq

Title   : subseq
Usage   : $s->subseq($start,$stop)
Function: generate a subsequence
Returns : a Bio::DB::GFF::Segment object
Args    : start and end of subsequence
Status  : Public

This method generates a new segment from the start and end positions given in the arguments. If stop < start, then the strand is reversed.

seq

Title   : seq
Usage   : $s->seq
Function: get the sequence string for this segment
Returns : a Bio::PrimarySeq
Args    : none
Status  : Public

Returns the sequence for this segment as a Bio::PrimarySeq. (-) strand segments are automatically reverse complemented

The method is called dna() return the data as a simple sequence string.

dna

Title   : dna
Usage   : $s->dna
Function: get the DNA string for this segment
Returns : a string
Args    : none
Status  : Public

Returns the sequence for this segment as a simple string. (-) strand segments are automatically reverse complemented

The method is also called protein().

primary_seq

Title   : primary_seq
Usage   : $s->primary_seq
Function: returns a Bio::PrimarySeqI compatible object
Returns : a Bio::PrimarySeqI object
Args    : none
Status  : Public

This is for compatibility with BioPerl's separation of SeqI from PrimarySeqI. It just returns itself.

type

Title   : type
Usage   : $s->type
Function: return the string "feature"
Returns : the string "feature"
Args    : none
Status  : Public

This is for future sequence ontology-compatibility and represents the default type of a feature on the genome

equals

Title   : equals
Usage   : $s->equals($d)
Function: segment equality
Returns : true, if two segments are equal
Args    : another segment
Status  : Public

Returns true if the two segments have the same source sequence, start and stop.

asString

Title   : asString
Usage   : $s->asString
Function: human-readable string for segment
Returns : a string
Args    : none
Status  : Public

Returns a human-readable string representing this sequence. Format is:

sourceseq/start,stop

clone

Title   : clone
Usage   : $copy = $s->clone
Function: make a copy of this segment
Returns : a Bio::DB::GFF::Segment object
Args    : none
Status  : Public

This method creates a copy of the segment and returns it.

error

Title   : error
Usage   : $error = $s->error([$new_error])
Function: get or set the last error
Returns : a string
Args    : an error message (optional)
Status  : Public

In case of a fault, this method can be used to obtain the last error message. Internally it is called to set the error message.

Relative Addressing Methods

The following methods are provided for compatibility with Bio::DB::GFF::RelSegment, which provides relative addressing functions.

abs_start

Title   : abs_start
Usage   : $s->abs_start
Function: the absolute start of the segment
Returns : an integer
Args    : none
Status  : Public

This is an alias to start(), and provided for API compatibility with Bio::DB::GFF::RelSegment.

abs_end

Title   : abs_end
Usage   : $s->abs_end
Function: the absolute stop of the segment
Returns : an integer
Args    : none
Status  : Public

This is an alias to stop(), and provided for API compatibility with Bio::DB::GFF::RelSegment.

abs_strand

Title   : abs_strand
Usage   : $s->abs_strand
Function: the absolute strand of the segment
Returns : +1,0,-1
Args    : none
Status  : Public

This is an alias to strand(), and provided for API compatibility with Bio::DB::GFF::RelSegment.

abs_ref

Title   : abs_ref
Usage   : $s->abs_ref
Function: the reference sequence for this segment
Returns : a string
Args    : none
Status  : Public

This is an alias to sourceseq(), and is here to provide API compatibility with Bio::DB::GFF::RelSegment.

refseq

Title   : refseq
Usage   : $s->refseq
Function: get or set the reference sequence
Returns : a string
Args    : none
Status  : Public

Examine or change the reference sequence. This is an alias to sourceseq(), provided here for API compatibility with Bio::DB::GFF::RelSegment.

ref

Title   : ref
Usage   : $s->refseq
Function: get or set the reference sequence
Returns : a string
Args    : none
Status  : Public

An alias for refseq()

seq_id

Title   : seq_id
Usage   : $ref = $s->seq_id
Function: get the reference sequence in a LocationI-compatible way
Returns : a string
Args    : none
Status  : Public

An alias for refseq() but only allows reading.

truncated

Title   : truncated
Usage   : $truncated = $s->truncated
Function: Flag indicating that the segment was truncated during creation
Returns : A boolean flag
Args    : none
Status  : Public

This indicates that the sequence was truncated during creation. The returned flag is undef if no truncation occured. If truncation did occur, the flag is actually an array ref in which the first element is true if truncation occurred on the left, and the second element occurred if truncation occurred on the right.

Bio::RangeI Methods

The following Bio::RangeI methods are supported:

overlaps(), contains(), equals(),intersection(),union(),overlap_extent()

Bio::SeqI implementation

primary_id

Title   : primary_id
Usage   : $unique_implementation_key = $obj->primary_id;
Function: Returns the unique id for this object in this
          implementation. This allows implementations to manage their
          own object ids in a way the implementaiton can control
          clients can expect one id to map to one object.

          For sequences with no accession number, this method should
          return a stringified memory location.

Returns : A string
Args    : None
Status  : Virtual

display_name

Title   : display_name
Usage   : $id = $obj->display_name or $obj->display_name($newid);
Function: Gets or sets the display id, also known as the common name of
          the Seq object.

          The semantics of this is that it is the most likely string
          to be used as an identifier of the sequence, and likely to
          have "human" readability.  The id is equivalent to the LOCUS
          field of the GenBank/EMBL databanks and the ID field of the
          Swissprot/sptrembl database. In fasta format, the >(\S+) is
          presumed to be the id, though some people overload the id
          to embed other information. Bioperl does not use any
          embedded information in the ID field, and people are
          encouraged to use other mechanisms (accession field for
          example, or extending the sequence object) to solve this.

          Notice that $seq->id() maps to this function, mainly for
          legacy/convenience issues.
Returns : A string
Args    : None or a new id

Note, this used to be called display_id(), and this name is preserved for backward compatibility. The default is to return the seq_id().

accession_number

Title   : accession_number
Usage   : $unique_biological_key = $obj->accession_number;
Function: Returns the unique biological id for a sequence, commonly
          called the accession_number. For sequences from established
          databases, the implementors should try to use the correct
          accession number. Notice that primary_id() provides the
          unique id for the implemetation, allowing multiple objects
          to have the same accession number in a particular implementation.

          For sequences with no accession number, this method should return
          "unknown".
Returns : A string
Args    : None

alphabet

Title   : alphabet
Usage   : if( $obj->alphabet eq 'dna' ) { /Do Something/ }
Function: Returns the type of sequence being one of
          'dna', 'rna' or 'protein'. This is case sensitive.

          This is not called <type> because this would cause
          upgrade problems from the 0.5 and earlier Seq objects.

Returns : a string either 'dna','rna','protein'. NB - the object must
          make a call of the type - if there is no type specified it
          has to guess.
Args    : none
Status  : Virtual

desc

Title   : desc
Usage   : $seqobj->desc($string) or $seqobj->desc()
Function: Sets or gets the description of the sequence
Example :
Returns : The description
Args    : The description or none

species

Title   : species
Usage   : $species = $seq->species() or $seq->species($species)
Function: Gets or sets the species
Example :
Returns : Bio::Species object
Args    : None or Bio::Species object

See Bio::Species for more information

annotation

Title   : annotation
Usage   : $ann = $seq->annotation or $seq->annotation($annotation)
Function: Gets or sets the annotation
Example :
Returns : Bio::Annotation object
Args    : None or Bio::Annotation object

See Bio::Annotation for more information

is_circular

Title   : is_circular
Usage   : if( $obj->is_circular) { /Do Something/ }
Function: Returns true if the molecule is circular
Returns : Boolean value
Args    : none

BUGS

Report them please.

SEE ALSO

bioperl

AUTHOR

Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2001 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

CONTRIBUTORS

Jason Stajich <jason@bioperl.org>.

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq