Bio SeqI
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Summary
Bio::SeqI - [Developers] Abstract Interface of Sequence (with features)
Package variables
No package variables defined.
Inherit
Bio::AnnotatableI Bio::FeatureHolderI Bio::PrimarySeqI
Synopsis
    # Bio::SeqI is the interface class for sequences.
# If you are a newcomer to bioperl, you should # start with Bio::Seq documentation. This # documentation is mainly for developers using # Bioperl. # Bio::SeqI implements Bio::PrimarySeqI $seq = $seqobj->seq(); # actual sequence as a string $seqstr = $seqobj->subseq(10,50); # Bio::SeqI has annotationcollections $ann = $seqobj->annotation(); # annotation object # Bio::SeqI has sequence features # features must implement Bio::SeqFeatureI @features = $seqobj->get_SeqFeatures(); # just top level @features = $seqobj->get_all_SeqFeatures(); # descend into sub features
Description
Bio::SeqI is the abstract interface of annotated Sequences. These
methods are those which you can be guaranteed to get for any Bio::SeqI.
For most users of the package the documentation (and methods) in this
class are not at useful - this is a developers only class which
defines what methods have to be implemented by other Perl objects to
comply to the Bio::SeqI interface. Go "perldoc Bio::Seq" or "man
Bio::Seq" for more information.
There aren't many method here, because too many complicated functions here
would prevent implementations which are just wrappers around a database or
similar delayed mechanisms.
Most of the clever stuff happens inside the SeqFeatureI system.
A good reference implementation is Bio::Seq which is a pure perl
implementation of this class with a lot of extra pieces for extra
manipulation. However, if you want to be able to use any sequence
object in your analysis, if you can do it just using these methods,
then you know you will be future proof and compatible with other
implementations of Seq.
Methods
seqDescriptionCode
write_GFFDescriptionCode
speciesDescriptionCode
primary_seqDescriptionCode
Methods description
seqcode    nextTop
 Title   : seq
Usage : my $string = $seq->seq();
Function: Retrieves the sequence string for the sequence object
Returns : string
Args : none
write_GFFcodeprevnextTop
 Title   : write_GFF
Usage : $seq->write_GFF(\*FILEHANDLE);
Function: Convenience method to write out all the sequence features
in GFF format to the provided filehandle (STDOUT by default)
Returns : none
Args : [optional] filehandle to write to (default is STDOUT)
speciescodeprevnextTop
 Title   : species
Usage :
Function: Gets or sets the species
Example : my $species = $seq->species();
Returns : Bio::Species object
Args : Bio::Species object or none;
See Bio::Species for more information
primary_seqcodeprevnextTop
 Title   : primary_seq
Usage : my $primaryseq = $seq->primary_seq($newval)
Function: Retrieve the underlying Bio::PrimarySeqI object if available.
This is in the event one has a sequence with lots of features
but want to be able to narrow the object to just one with
the basics of a sequence (no features or annotations).
Returns : Bio::PrimarySeqI
Args : Bio::PrimarySeqI or none;
See Bio::PrimarySeqI for more information
Methods code
seqdescriptionprevnextTop
sub seq {
   my ($self) = @_;
   $self->throw_not_implemented();
}
write_GFFdescriptionprevnextTop
sub write_GFF {
   my ($self,$fh) = @_;

   $fh || do { $fh =\* STDOUT; };

   foreach my $sf ( $self->get_all_SeqFeatures() ) {
       print $fh $sf->gff_string, "\n";
   }
}
speciesdescriptionprevnextTop
sub species {
    my ($self) = @_;
    $self->throw_not_implemented();
}
primary_seqdescriptionprevnextTop
sub primary_seq {
    my ($self) = @_;
    $self->throw_not_implemented;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
SupportTop
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan BirneyTop
Email birney@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
get_SeqFeaturesTop
 Title   : get_SeqFeatures
Usage : my @feats = $seq->get_SeqFeatures();
Function: retrieve just the toplevel sequence features attached to this seq
Returns : array of Bio::SeqFeatureI objects
Args : none
This method comes through extension of Bio::FeatureHolderI. See
Bio::FeatureHolderI and Bio::SeqFeatureI for more information.
get_all_SeqFeaturesTop
 Title   : get_all_SeqFeatures
Usage : my @feats = $seq->get_all_SeqFeatures();
Function: returns all SeqFeatures, including sub SeqFeatures
Returns : an array of Bio::SeqFeatureI objects
Args : none
This method comes through extension of Bio::FeatureHolderI. See
Bio::FeatureHolderI and Bio::SeqFeatureI for more information.
feature_countTop
 Title   : feature_count
Usage : my $count = $seq->feature_count();
Function: Return the number of SeqFeatures attached to a sequence
Returns : integer representing the number of SeqFeatures
Args : none
This method comes through extension of Bio::FeatureHolderI. See
Bio::FeatureHolderI for more information.
annotationTop
 Title   : annotation
Usage : my $ann = $seq->annotation($seq_obj);
Function: retrieve the attached annotation object
Returns : Bio::AnnotationCollectionI or none;
See Bio::AnnotationCollectionI and Bio::Annotation::Collection
for more information. This method comes through extension from
Bio::AnnotatableI.