man Bio::SeqFeature::Lite (3): Lightweight Bio::SeqFeatureI class

SYNOPSIS

# create a simple feature with no internal structure
$f = Bio::SeqFeature::Lite->new(-start => 1000,
-stop => 2000,
-type => 'transcript',
-name => 'alpha-1 antitrypsin',
-desc => 'an enzyme inhibitor',
);
# create a feature composed of multiple segments, all of type "similarity"
$f = Bio::SeqFeature::Lite->new(-segments => [[1000,1100],[1500,1550],[1800,2000]],
-name => 'ABC-3',
-type => 'gapped_alignment',
-subtype => 'similarity');
# build up a gene exon by exon
$e1 = Bio::SeqFeature::Lite->new(-start=>1,-stop=>100,-type=>'exon');
$e2 = Bio::SeqFeature::Lite->new(-start=>150,-stop=>200,-type=>'exon');
$e3 = Bio::SeqFeature::Lite->new(-start=>300,-stop=>500,-type=>'exon');
$f = Bio::SeqFeature::Lite->new(-segments=>[$e1,$e2,$e3],-type=>'gene');

DESCRIPTION

This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing.

All methods are as described in Bio::SeqFeatureI with the following additions:

The new() Constructor

 $feature = Bio::SeqFeature::Lite->new(@args);

This method creates a new feature object. You can create a simple feature that contains no subfeatures, or a hierarchically nested object.

Arguments are as follows:

  -seq_id      the reference sequence
  -start       the start position of the feature
  -end         the stop position of the feature
  -stop        an alias for end
  -name        the feature name (returned by seqname())
  -type        the feature type (returned by primary_tag())
  -primary_tag the same as -type
  -source      the source tag
  -score       the feature score (for GFF compatibility)
  -desc        a description of the feature
  -segments    a list of subfeatures (see below)
  -subtype     the type to use when creating subfeatures
  -strand      the strand of the feature (one of -1, 0 or +1)
  -phase       the phase of the feature (0..2)
  -seq         a dna or protein sequence string to attach to feature
  -id          an alias for -name
  -seqname     an alias for -name
  -display_id  an alias for -name
  -display_name an alias for -name  (do you get the idea the API has changed?)
  -primary_id  unique database ID
  -url         a URL to link to when rendered with Bio::Graphics
  -attributes  a hashref of tag value attributes, in which the key is the tag
               and the value is an array reference of values
  -factory     a reference to a feature factory, used for compatibility with
               more obscure parts of Bio::DB::GFF

The subfeatures passed in -segments may be an array of Bio::SeqFeature::Lite objects, or an array of [$start,$stop] pairs. Each pair should be a two-element array reference. In the latter case, the feature type passed in -subtype will be used when creating the subfeatures.

If no feature type is passed, then it defaults to ``feature''.

Non-SeqFeatureI methods

A number of new methods are provided for compatibility with Ace::Sequence, which has a slightly different API from SeqFeatureI:

url(): Get/set the URL that the graphical rendering of this feature will link to.
add_segment(@segments): Add one or more segments (a subfeature). Segments can either be Feature objects, or [start,stop] arrays, as in the -segments argument to new(). The feature endpoints are automatically adjusted.
segments(): An alias for sub_SeqFeature().
get_SeqFeatures(): Alias for sub_SeqFeature()
get_all_SeqFeatures(): Alias for sub_SeqFeature()
merged_segments(): Another alias for sub_SeqFeature().
stop(): An alias for end().
name(): An alias for seqname().
exons(): An alias for sub_SeqFeature() (you don't want to know why!)

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

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

location

 Title   : location
 Usage   : my $location = $seqfeature->location()
 Function: returns a location object suitable for identifying location
           of feature on sequence or parent feature
 Returns : Bio::LocationI object
 Args    : none

location_string

 Title   : location_string
 Usage   : my $string = $seqfeature->location_string()
 Function: Returns a location string in a format recognized by gbrowse
 Returns : a string
 Args    : none

This is a convenience function used by the generic genome browser. It returns the location of the feature and its subfeatures in the compact form ``start1..end1,start2..end2,...''. Use $seqfeature->location()->toFTString() to obtain a standard GenBank/EMBL location representation.

clone

 Title   : clone
 Usage   : my $feature = $seqfeature->clone
 Function: Create a deep copy of the feature
 Returns : A copy of the feature
 Args    : none

refseq

 Title   : refseq
 Usage   : $ref = $s->refseq([$newseq] [,$newseqclass])
 Function: get/set reference sequence
 Returns : current reference sequence
 Args    : new reference sequence and class (optional)
 Status  : Public

This method will get or set the reference sequence. Called with no arguments, it returns the current reference sequence. Called with any Bio::SeqFeatureI object that provides the seq_id(), start(), end() and strand() methods.

The method will generate an exception if you attempt to set the reference sequence to a sequence that has a different seq_id from the current feature.

AUTHOR

Lincoln Stein <[email protected]>.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.