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Bio::SeqFeature::Generic.3pm

NAME

Bio::SeqFeature::Generic - Generic SeqFeature

SYNOPSIS

    $feat = Bio::SeqFeature::Generic->new( 
             -start        => 10, 
             -end          => 100,
             -strand       => -1, 
             -primary      => 'repeat', # -primary_tag is a synonym
             -source_tag   => 'repeatmasker',
             -display_name => 'alu family',
             -score        => 1000,
             -tag          => { new => 1,
                                author => 'someone',
                                sillytag => 'this is silly!' } );
 
    $feat = Bio::SeqFeature::Generic->new( -gff_string => $string );
    # if you want explicitly GFF1
    $feat = Bio::SeqFeature::Generic->new( -gff1_string => $string );
 
    # add it to an annotated sequence
 
    $annseq->add_SeqFeature($feat);
 
 

DESCRIPTION

Bio::SeqFeature::Generic is a generic implementation for the Bio::SeqFeatureI interface, providing a simple object to provide all the information for a feature on a sequence.

For many Features, this is all you will need to use (for example, this is fine for Repeats in DNA sequence or Domains in protein sequence). For other features, which have more structure, this is a good base class to extend using inheritence to have new things: this is what is done in the Bio::SeqFeature::Gene, Bio::SeqFeature::Transcript and Bio::SeqFeature::Exon, which provide well coordinated classes to represent genes on DNA sequence (for example, you can get the protein sequence out from a transcript class).

For many Features, you want to add some piece of information, for example a common one is that this feature is 'new' whereas other features are 'old'. The tag system, which here is implemented using a hash can be used here. You can use the tag system to extend the Bio::SeqFeature::Generic programmatically: that is, you know that you have read in more information into the tag 'mytag' which you can then retrieve. This means you do not need to know how to write inherited Perl to provide more complex information on a feature, and/or, if you do know but you do not want to write a new class every time you need some extra piece of information, you can use the tag system to easily store and then retrieve information.

The tag system can be written in/out of GFF format, and also into EMBL format via the Bio::SeqIO system

Implemented Interfaces

This class implementes the following interfaces.

Bio::SeqFeatureI

Note that this includes implementing Bio::RangeI.

Bio::AnnotatableI

Bio::FeatureHolderI

Features held by a feature are essentially sub-features.

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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Ewan Birney

Ewan Birney <birney@sanger.ac.uk>

DEVELOPERS

This class has been written with an eye out for inheritance. The fields the actual object hash are:

    _gsf_tag_hash  = reference to a hash for the tags
    _gsf_sub_array = reference to an array for subfeatures
 
 

APPENDIX

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

set_attributes

  Title   : set_attributes
  Usage   :
  Function: Sets a whole array of parameters at once.
  Example :
  Returns : none
  Args    : Named parameters, in the form as they would otherwise be passed
            to new(). Currently recognized are:
 
                     -start          start position
                     -end            end position
                     -strand         strand
                     -primary_tag    primary tag 
                     -primary        (synonym for -primary_tag)
                     -source         source tag
                     -frame          frame
                     -score          score value
                     -tag            a reference to a tag/value hash
                     -gff_string     GFF v.2 string to initialize from
                     -gff1_string    GFF v.1 string to initialize from
                     -seq_id         the display name of the sequence
                     -annotation     the AnnotationCollectionI object
                     -location       the LocationI object
 
 

direct_new

  Title   : direct_new
  Usage   : my $obj = Bio::SeqFeature::Generic->direct_new
  Function: create a blessed hash - for performance improvement in 
            object creation
  Returns : Bio::SeqFeature::Generic object
  Args    : 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    : [optional] Bio::LocationI object to set the value to.
 
 

start

  Title   : start
  Usage   : $start = $feat->start
            $feat->start(20)
  Function: Get/set on the start coordinate of the feature
  Returns : integer
  Args    : none
 
 

end

  Title   : end
  Usage   : $end = $feat->end
            $feat->end($end)
  Function: get/set on the end coordinate of the feature
  Returns : integer
  Args    : none
 
 

length

  Title   : length
  Usage   : my $len = $feature->length
  Function: Get the feature length computed as 
            $feat->end - $feat->start + 1
  Returns : integer
  Args    : none
 
 

strand

  Title   : strand
  Usage   : $strand = $feat->strand()
            $feat->strand($strand)
  Function: get/set on strand information, being 1,-1 or 0
  Returns : -1,1 or 0
  Args    : none
 
 

score

  Title   : score
  Usage   : $score = $feat->score()
            $feat->score($score)
  Function: get/set on score information
  Returns : float
  Args    : none if get, the new value if set
 
 

frame

  Title   : frame
  Usage   : $frame = $feat->frame()
            $feat->frame($frame)
  Function: get/set on frame information
  Returns : 0,1,2, '.'
  Args    : none if get, the new value if set
 
 

primary_tag

  Title   : primary_tag
  Usage   : $tag = $feat->primary_tag()
            $feat->primary_tag('exon')
  Function: get/set on the primary tag for a feature,
            eg 'exon'
  Returns : a string
  Args    : none
 
 

source_tag

  Title   : source_tag
  Usage   : $tag = $feat->source_tag()
            $feat->source_tag('genscan');
  Function: Returns the source tag for a feature,
            eg, 'genscan'
  Returns : a string
  Args    : none
 
 

has_tag

  Title   : has_tag
  Usage   : $value = $self->has_tag('some_tag')
  Function: Tests wether a feature contaings a tag
  Returns : TRUE if the SeqFeature has the tag,
            and FALSE otherwise.
  Args    : The name of a tag
 
 

add_tag_value

  Title   : add_tag_value
  Usage   : $self->add_tag_value('note',"this is a note");
  Returns : TRUE on success
  Args    : tag (string) and one or more values (any scalar(s))
 
 

get_tag_values

  Title   : get_tag_values
  Usage   : @values = $gsf->get_tag_values('note');
  Function: Returns a list of all the values stored
            under a particular tag.
  Returns : A list of scalars
  Args    : The name of the tag
 
 

get_all_tags

  Title   : get_all_tags
  Usage   : @tags = $feat->get_all_tags()
  Function: Get a list of all the tags in a feature
  Returns : An array of tag names
  Args    : none
 
 

# added a sort so that tags will be returned in a predictable order # I still think we should be able to specify a sort function # to the object at some point # -js

remove_tag

  Title   : remove_tag
  Usage   : $feat->remove_tag('some_tag')
  Function: removes a tag from this feature
  Returns : the array of values for this tag before removing it
  Args    : tag (string)
 
 

attach_seq

  Title   : attach_seq
  Usage   : $sf->attach_seq($seq)
  Function: Attaches a Bio::Seq object to this feature. This
            Bio::Seq object is for the *entire* sequence: ie
            from 1 to 10000
  Example :
  Returns : TRUE on success
  Args    : a Bio::PrimarySeqI compliant object
 
 

seq

  Title   : seq
  Usage   : $tseq = $sf->seq()
  Function: returns the truncated sequence (if there) for this
  Example :
  Returns : sub seq (a Bio::PrimarySeqI compliant object) on attached sequence
            bounded by start & end, or undef if there is no sequence attached
  Args    : none
 
 

entire_seq

  Title   : entire_seq
  Usage   : $whole_seq = $sf->entire_seq()
  Function: gives the entire sequence that this seqfeature is attached to
  Example :
  Returns : a Bio::PrimarySeqI compliant object, or undef if there is no
            sequence attached
  Args    :
 
 

seq_id

  Title   : seq_id
  Usage   : $obj->seq_id($newval)
  Function: There are many cases when you make a feature that you
            do know the sequence name, but do not know its actual
            sequence. This is an attribute such that you can store
            the ID (e.g., display_id) of the sequence.
 
            This attribute should *not* be used in GFF dumping, as
            that should come from the collection in which the seq
            feature was found.
  Returns : value of seq_id
  Args    : newvalue (optional)
 
 

display_name

  Title   : display_name
  Usage   : $featname = $obj->display_name
  Function: Implements the display_name() method, which is a human-readable
            name for the feature. 
  Returns : value of display_name (a string)
  Args    : Optionally, on set the new value or undef
 
 

Methods for implementing Bio::AnnotatableI

annotation

  Title   : annotation
  Usage   : $obj->annotation($annot_obj)
  Function: Get/set the annotation collection object for annotating this
            feature.
 
  Example : 
  Returns : A Bio::AnnotationCollectionI object
  Args    : newvalue (optional)
 
 

Methods to implement Bio::FeatureHolderI

This includes methods for retrieving, adding, and removing features. Since this is already a feature, features held by this feature holder are essentially sub-features.

get_SeqFeatures

  Title   : get_SeqFeatures
  Usage   : @feats = $feat->get_SeqFeatures();
  Function: Returns an array of sub Sequence Features
  Returns : An array
  Args    : none
 
 

add_SeqFeature

  Title   : add_SeqFeature
  Usage   : $feat->add_SeqFeature($subfeat);
            $feat->add_SeqFeature($subfeat,'EXPAND')
  Function: Adds a SeqFeature into the subSeqFeature array.
            With no 'EXPAND' qualifer, subfeat will be tested
            as to whether it lies inside the parent, and throw
            an exception if not.
 
            If EXPAND is used, the parent's start/end/strand will
            be adjusted so that it grows to accommodate the new
            subFeature
  Returns : nothing
  Args    : An object which has the SeqFeatureI interface
 
 

remove_SeqFeatures

  Title   : remove_SeqFeatures
  Usage   : $sf->remove_SeqFeatures
  Function: Removes all SeqFeatures
 
            If you want to remove only a subset of features then remove that 
            subset from the returned array, and add back the rest.
  Example :
  Returns : The array of Bio::SeqFeatureI implementing features that was
            deleted.
  Args    : none
 
 

GFF-related methods

gff_format

  Title   : gff_format
  Usage   : # get:
            $gffio = $feature->gff_format();
            # set (change the default version of GFF2):
            $feature->gff_format(Bio::Tools::GFF->new(-gff_version => 1));
  Function: Get/set the GFF format interpreter. This object is supposed to 
            format and parse GFF. See Bio::Tools::GFF for the interface.
 
            If this method is called as class method, the default for all
            newly created instances will be changed. Otherwise only this
            instance will be affected.
  Example : 
  Returns : a Bio::Tools::GFF compliant object
  Args    : On set, an instance of Bio::Tools::GFF or a derived object.
 
 

gff_string

  Title   : gff_string
  Usage   : $str = $feat->gff_string;
            $str = $feat->gff_string($gff_formatter);
  Function: Provides the feature information in GFF format.
 
            We override this here from Bio::SeqFeatureI in order to use the
            formatter returned by gff_format().
 
  Returns : A string
  Args    : Optionally, an object implementing gff_string().
 
 

slurp_gff_file

  Title   : slurp_file
  Usage   : @features = Bio::SeqFeature::Generic::slurp_gff_file(\*FILE);
  Function: Sneaky function to load an entire file as in memory objects.
            Beware of big files.
 
            This method is deprecated. Use Bio::Tools::GFF instead, which can
            also handle large files.
 
  Example :
  Returns :
  Args    :
 
 

_from_gff_string

  Title   : _from_gff_string
  Usage   :
  Function: Set feature properties from GFF string. 
 
            This method uses the object returned by gff_format() for the
            actual interpretation of the string. Set a different GFF format
            interpreter first if you need a specific version, like GFF1. (The
            default is GFF2.)
  Example :
  Returns : 
  Args    : a GFF-formatted string
 
 

_expand_region

  Title   : _expand_region
  Usage   : $self->_expand_region($feature);
  Function: Expand the total region covered by this feature to
            accomodate for the given feature.
 
            May be called whenever any kind of subfeature is added to this
            feature. add_sub_SeqFeature() already does this.
  Returns : 
  Args    : A Bio::SeqFeatureI implementing object.
 
 

_parse

  Title   : _parse
  Usage   :
  Function: Parsing hints
  Example :
  Returns :
  Args    :
 
 

_tag_value

  Title   : _tag_value
  Usage   : 
  Function: For internal use only. Convenience method for those tags that
            may only have a single value.
  Returns : The first value under the given tag as a scalar (string)
  Args    : The tag as a string. Optionally, the value on set.