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Bio::SeqFeature::PositionProxy.3pm

NAME

Bio::SeqFeature::PositionProxy - handle features when truncation/revcom sequences span a feature

SYNOPSIS

    $proxy = Bio::SeqFeature::PositionProxy->new( -loc => $loc,
                                                  -parent => $basefeature);
 
    $seq->add_SeqFeature($feat);
 
 

DESCRIPTION

PositionProxy is a Proxy Sequence Feature to handle truncation and revcomp without duplicating all the data within the sequence features. It holds a new location for a sequence feature and the original feature it came from to provide the additional annotation information.

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 of inheritence. 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 sub arrays
    _gsf_start     = scalar of the start point
    _gsf_end       = scalar of the end point
    _gsf_strand    = scalar of the strand
 
 

APPENDIX

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

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
 
 

parent

  Title   : parent
  Usage   : my $sf = $proxy->parent()
  Function: returns the seqfeature parent of this proxy
  Returns : Bio::SeqFeatureI object
  Args    : none
 
 

start

  Title   : start
  Usage   : $start = $feat->start
            $feat->start(20)
  Function: Get
  Returns : integer
  Args    : none
 
 

end

  Title   : end
  Usage   : $end = $feat->end
            $feat->end($end)
  Function: get
  Returns : integer
  Args    : none
 
 

length

  Title   : length
  Usage   :
  Function:
  Example :
  Returns :
  Args    :
 
 

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
 
 

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    :
 
 

seq

  Title   : seq
  Usage   : $tseq = $sf->seq()
  Function: returns the truncated sequence (if there) for this
  Example :
  Returns : sub seq on attached sequence bounded by start & end
  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 :
  Args    :
 
 

seqname

  Title   : seqname
  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 seqname.
 
            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 seqname
  Args    : newvalue (optional)
 
 

Proxies

These functions chain back to the parent for all non sequence related stuff.

primary_tag

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

source_tag

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

has_tag

  Title   : has_tag
  Usage   : $tag_exists = $self->has_tag('some_tag')
  Function: 
  Returns : TRUE if the specified tag exists, and FALSE otherwise
  Args    :
 
 

each_tag_value

  Title   : each_tag_value
  Usage   : @values = $self->each_tag_value('some_tag')
  Function: 
  Returns : An array comprising the values of the specified tag.
  Args    :
 
 

all_tags

  Title   : all_tags
  Usage   : @tags = $feat->all_tags()
  Function: gives all tags for this feature
  Returns : an array of strings
  Args    : none