Raw content of Bio::SeqFeatureI # $Id: SeqFeatureI.pm,v 2003/08/28 19:29:34 jason Exp $ # # BioPerl module for Bio::SeqFeatureI # # Cared for by Ewan Birney <birney@sanger.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqFeatureI - Abstract interface of a Sequence Feature =head1 SYNOPSIS # get a seqfeature somehow, eg, foreach $feat ( $seq->top_SeqFeatures() ) { print "Feature from ", $feat->start, "to ", $feat->end, " Primary tag ", $feat->primary_tag, ", produced by ", $feat->source_tag(), "\n"; if( $feat->strand == 0 ) { print "Feature applicable to either strand\n"; } else { print "Feature on strand ", $feat->strand,"\n"; # -1,1 } foreach $tag ( $feat->all_tags() ) { print "Feature has tag ", $tag, "with values, ", join(' ',$feat->each_tag_value($tag)), "\n"; } print "new feature\n" if $feat->has_tag('new'); # features can have sub features my @subfeat = $feat->get_SeqFeatures(); } =head1 DESCRIPTION This interface is the functions one can expect for any Sequence Feature, whatever its implementation or whether it is a more complex type (eg, a Gene). This object doesn\'t actually provide any implemention, it just provides the definitions of what methods one can call. See Bio::SeqFeature::Generic for a good standard implementation of this object =head1 FEEDBACK 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://bio.perl.org/MailList.html - About the mailing lists =head2 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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeatureI; use vars qw(@ISA $HasInMemory); use strict; BEGIN { eval { require Bio::DB::InMemoryCache }; if( $@ ) { $HasInMemory = 0 } else { $HasInMemory = 1 } } use Bio::RangeI; use Bio::Seq; use Carp; @ISA = qw(Bio::RangeI); =head1 SeqFeatureI specific methods New method interfaces. =cut =head2 get_SeqFeatures Title : get_SeqFeatures Usage : @feats = $feat->get_SeqFeatures(); Function: Returns an array of sub Sequence Features Returns : An array Args : none =cut sub get_SeqFeatures{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 display_name Title : display_name Usage : $name = $feat->display_name() Function: Returns the human-readable name of the feature for displays. Returns : a string Args : none =cut sub display_name { shift->throw_not_implemented(); } =head2 primary_tag Title : primary_tag Usage : $tag = $feat->primary_tag() Function: Returns the primary tag for a feature, eg 'exon' Returns : a string Args : none =cut sub primary_tag{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 source_tag Title : source_tag Usage : $tag = $feat->source_tag() Function: Returns the source tag for a feature, eg, 'genscan' Returns : a string Args : none =cut sub source_tag{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 has_tag Title : has_tag Usage : $tag_exists = $self->has_tag('some_tag') Function: Returns : TRUE if the specified tag exists, and FALSE otherwise Args : =cut sub has_tag{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 get_tag_values Title : get_tag_values Usage : @values = $self->get_tag_values('some_tag') Function: Returns : An array comprising the values of the specified tag. Args : =cut sub get_tag_values { shift->throw_not_implemented(); } =head2 get_all_tags Title : get_all_tags Usage : @tags = $feat->get_all_tags() Function: gives all tags for this feature Returns : an array of strings Args : none =cut sub get_all_tags{ shift->throw_not_implemented(); } =head2 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 Note that it is not guaranteed that if you obtain a feature from an object in bioperl, it will have a sequence attached. Also, implementors of this interface can choose to provide an empty implementation of this method. I.e., there is also no guarantee that if you do attach a sequence, seq() or entire_seq() will not return undef. The reason that this method is here on the interface is to enable you to call it on every SeqFeatureI compliant object, and that it will be implemented in a useful way and set to a useful value for the great majority of use cases. Implementors who choose to ignore the call are encouraged to specifically state this in their documentation. Example : Returns : TRUE on success Args : a Bio::PrimarySeqI compliant object =cut sub attach_seq { shift->throw_not_implemented(); } =head2 seq Title : seq Usage : $tseq = $sf->seq() Function: returns the truncated sequence (if there is a sequence attached) for this feature 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 =cut sub seq { shift->throw_not_implemented(); } =head2 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 : none =cut sub entire_seq { shift->throw_not_implemented(); } =head2 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) =cut sub seq_id { shift->throw_not_implemented(); } =head2 gff_string Title : gff_string Usage : $str = $feat->gff_string; $str = $feat->gff_string($gff_formatter); Function: Provides the feature information in GFF format. The implementation provided here returns GFF2 by default. If you want a different version, supply an object implementing a method gff_string() accepting a SeqFeatureI object as argument. E.g., to obtain GFF1 format, do the following: my $gffio = Bio::Tools::GFF->new(-gff_version => 1); $gff1str = $feat->gff_string($gff1io); Returns : A string Args : Optionally, an object implementing gff_string(). =cut sub gff_string{ my ($self,$formatter) = @_; $formatter = $self->_static_gff_formatter unless $formatter; return $formatter->gff_string($self); } my $static_gff_formatter = undef; =head2 _static_gff_formatter Title : _static_gff_formatter Usage : Function: Example : Returns : Args : =cut sub _static_gff_formatter{ my ($self,@args) = @_; if( !defined $static_gff_formatter ) { $static_gff_formatter = Bio::Tools::GFF->new('-gff_version' => 2); } return $static_gff_formatter; } =head1 Bio::RangeI methods List of interfaces inherited from Bio::RangeI (see L<Bio::RangeI> for details). =cut =head2 start Title : start Usage : $start = $feat->start Function: Returns the start coordinate of the feature Returns : integer Args : none =head2 end Title : end Usage : $end = $feat->end Function: Returns the end coordinate of the feature Returns : integer Args : none =head2 strand Title : strand Usage : $strand = $feat->strand() Function: Returns strand information, being 1,-1 or 0 Returns : -1,1 or 0 Args : none =cut =head1 Decorating methods These methods have an implementation provided by Bio::SeqFeatureI, but can be validly overwritten by subclasses =head2 spliced_seq Title : spliced_seq Usage : $seq = $feature->spliced_seq() $seq = $feature_with_remote_locations->spliced_seq($db_for_seqs) Function: Provides a sequence of the feature which is the most semantically "relevant" feature for this sequence. A default implementation is provided which for simple cases returns just the sequence, but for split cases, loops over the split location to return the sequence. In the case of split locations with remote locations, eg join(AB000123:5567-5589,80..1144) in the case when a database object is passed in, it will attempt to retrieve the sequence from the database object, and "Do the right thing", however if no database object is provided, it will generate the correct number of N's (DNA) or X's (protein, though this is unlikely). This function is deliberately "magical" attempting to second guess what a user wants as "the" sequence for this feature Implementing classes are free to override this method with their own magic if they have a better idea what the user wants Args : [optional] A Bio::DB::RandomAccessI compliant object Returns : A Bio::Seq =cut sub spliced_seq { my $self = shift; my $db = shift; if( ! $self->location->isa("Bio::Location::SplitLocationI") ) { return $self->seq(); # nice and easy! } # redundant test, but the above ISA is probably not ideal. if( ! $self->location->isa("Bio::Location::SplitLocationI") ) { $self->throw("not atomic, not split, yikes, in trouble!"); } my $seqstr; my $seqid = $self->entire_seq->display_id; # This is to deal with reverse strand features # so we are really sorting features 5' -> 3' on their strand # i.e. rev strand features will be sorted largest to smallest # as this how revcom CDSes seem to be annotated in genbank. # Might need to eventually allow this to be programable? # (can I mention how much fun this is NOT! --jason) my ($mixed,$mixedloc,$fstrand) = (0); if( defined $db && ref($db) && !$db->isa('Bio::DB::RandomAccessI') ) { $self->warn("Must pass in a valid Bio::DB::RandomAccessI object for access to remote locations for spliced_seq"); $db = undef; } elsif( defined $db && $HasInMemory && ! $db->isa('Bio::DB::InMemoryCache') ) { $db = new Bio::DB::InMemoryCache(-seqdb => $db); } if( $self->isa('Bio::Das::SegmentI') && ! $self->absolute ) { $self->warn("Calling spliced_seq with a Bio::Das::SegmentI ". "which does have absolute set to 1 -- be warned ". "you may not be getting things on the correct strand"); } my @locs = map { $_->[0] } # sort so that most negative is first basically to order # the features on the opposite strand 5'->3' on their strand # rather than they way most are input which is on the fwd strand sort { $a->[1] <=> $b->[1] } # Yes Tim, Schwartzian transformation map { $fstrand = $_->strand unless defined $fstrand; $mixed = 1 if defined $_->strand && $fstrand != $_->strand; if( defined $_->seq_id ) { $mixedloc = 1 if( $_->seq_id ne $seqid ); } [ $_, $_->start* ($_->strand || 1)]; } $self->location->each_Location; if ( $mixed ) { $self->warn("Mixed strand locations, spliced seq using the input ". "order rather than trying to sort"); @locs = $self->location->each_Location; } elsif( $mixedloc ) { # we'll use the prescribed location order @locs = $self->location->each_Location; } foreach my $loc ( @locs ) { if( ! $loc->isa("Bio::Location::Atomic") ) { $self->throw("Can only deal with one level deep locations"); } my $called_seq; if( $fstrand != $loc->strand ) { $self->warn("feature strand is different from location strand!"); } # deal with remote sequences if( defined $loc->seq_id && $loc->seq_id ne $seqid ) { if( defined $db ) { my $sid = $loc->seq_id; $sid =~ s/\.\d+$//g; eval { $called_seq = $db->get_Seq_by_acc($sid); }; if( $@ ) { $self->warn("In attempting to join a remote location, sequence $sid was not in database. Will provide padding N's. Full exception \n\n$@"); $called_seq = undef; } } else { $self->warn( "cannot get remote location for ".$loc->seq_id ." without a valid Bio::DB::RandomAccessI database handle (like Bio::DB::GenBank)"); $called_seq = undef; } if( !defined $called_seq ) { $seqstr .= 'N' x $self->length; next; } } else { $called_seq = $self->entire_seq; } if( $self->isa('Bio::Das::SegmentI') ) { my ($s,$e) = ($loc->start,$loc->end); $seqstr .= $called_seq->subseq($s,$e)->seq(); } else { # This is dumb subseq should work on locations... if( $loc->strand == 1 ) { $seqstr .= $called_seq->subseq($loc->start,$loc->end); } else { $seqstr .= $called_seq->trunc($loc->start,$loc->end)->revcom->seq(); } } } my $out = Bio::Seq->new( -id => $self->entire_seq->display_id . "_spliced_feat", -seq => $seqstr); return $out; } =head1 RangeI methods These methods are inherited from RangeI and can be used directly from a SeqFeatureI interface. Remember that a SeqFeature is-a RangeI, and so wherever you see RangeI you can use a feature ($r in the below documentation). =head2 overlaps Title : overlaps Usage : if($feat->overlaps($r)) { do stuff } if($feat->overlaps(200)) { do stuff } Function: tests if $feat overlaps $r Args : a RangeI to test for overlap with, or a point Returns : true if the Range overlaps with the feature, false otherwise =head2 contains Title : contains Usage : if($feat->contains($r) { do stuff } Function: tests whether $feat totally contains $r Args : a RangeI to test for being contained Returns : true if the argument is totaly contained within this range =head2 equals Title : equals Usage : if($feat->equals($r)) Function: test whether $feat has the same start, end, strand as $r Args : a RangeI to test for equality Returns : true if they are describing the same range =head1 Geometrical methods These methods do things to the geometry of ranges, and return triplets (start, stop, strand) from which new ranges could be built. =head2 intersection Title : intersection Usage : ($start, $stop, $strand) = $feat->intersection($r) Function: gives the range that is contained by both ranges Args : a RangeI to compare this one to Returns : nothing if they do not overlap, or the range that they do overlap =head2 union Title : union Usage : ($start, $stop, $strand) = $feat->union($r); : ($start, $stop, $strand) = Bio::RangeI->union(@ranges); Function: finds the minimal range that contains all of the ranges Args : a range or list of ranges to find the union of Returns : the range containing all of the ranges =cut =head2 location Title : location Usage : my $location = $seqfeature->location() Function: returns a location object suitable for identifying location of feature on sequence or parent feature Returns : Bio::LocationI object Args : none =cut sub location { my ($self) = @_; $self->throw_not_implemented(); } 1;