Bio
SeqI
Summary
Bio::SeqI - Abstract Interface of Sequence (with features)
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# get a Bio::SeqI somehow, eg, via SeqIO. See SeqIO info
# for more information
$seqio = Bio::SeqIO->new ( '-format' => 'Fasta' , -file => 'myfile.fasta');
$seqobj = $seqio->next_seq();
# features must implement Bio::SeqFeatureI
@features = $seqobj->top_SeqFeatures(); # just top level
@features = $seqobj->all_SeqFeatures(); # descend into sub features
$seq = $seqobj->seq(); # actual sequence as a string
$seqstr = $seqobj->subseq(10,50);
$ann = $seqobj->annotation(); # annotation object
Description
SeqI is the abstract interface of annotated Sequence. These methods
are those which you can be guarenteed to get for any annseq. There aren't
many here, because too many complicated functions here 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 alot 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
Methods description
Title : top_SeqFeatures
Usage : my @features = $seq->top_SeqFeatures();
Function: (may be deprecated in the future)
Returns : An array of top level sequence features,
features which contain features are NOT flattened
Args : none |
Title : all_SeqFeatures
Usage : @features = $annseq->all_SeqFeatures()
Function: returns all SeqFeatures, included sub SeqFeatures
Returns : an array
Args : none |
Title : seq
Usage : my $sequence = $seq->seq();
Function: Get/Set the sequence as a string
Returns : string
Args : (optional) sequence string to set
(if permitted by the implementation) |
Title : write_GFF
Usage : $seq->write_GFF(\*OUTPUTHANDLE);
Function: Utility methods which creates GFF output
Returns : none
Args : (optional) filehandle to write to (default is STDOUT) |
Title : annotation
Usage : $obj->annotation($seq_obj)
Function: Get/Set Annotation object associated with the sequence.
This is where features with no explicit location are aggregated.
Returns : Bio::AnnotationCollectionI object
Args : None or Bio::Annotation object
See Bio::AnnotationCollectionI and Bio::Annotation::Collection
for more information |
Title : feature_count
Usage : $seq->feature_count()
Function: Return the number of SeqFeatures attached to a sequence
Returns : number of SeqFeatures
Args : none |
Title : species
Usage : $species = $self->species();
Function: Gets or sets the species
Returns : Bio::Species object
Args : Bio::Species object or none; |
Title : primary_seq
Usage : $obj->primary_seq($newval)
Function: Get/Set the underlying primary sequence for a SeqI.
This cannot always be assumed some implementations
may not provide a primary sequence underneath.
Returns : value of primary_seq
Args : newvalue (optional) |
Methods code
sub top_SeqFeatures
{ my ($self) = @_;
$self->throw_not_implemented; } | sub all_SeqFeatures
{ my ($self) = @_;
$self->throw_not_implemented(); } | sub seq
{ my ($self) = @_;
$self->throw_not_implemented(); } | sub write_GFF
{ my ($self,$fh) = @_;
$fh || do { $fh =\* STDOUT; };
foreach my $sf ( $self->all_SeqFeatures() ) {
print $fh $sf->gff_string, "\n";
}} | sub annotation
{ my ($obj) = @_;
$obj->throw_not_implemented(); } | sub feature_count
{ my ($obj) = @_;
$obj->throw_not_implemented();} | sub species
{ my ($self) = @_;
$self->throw_not_implemented();} | sub primary_seq
{ my ($self) = @_;
$self->throw_not_implemented;} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
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Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
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bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _