Raw content of Bio::SeqFeature::Generic # $Id: Generic.pm,v 1.74.2.1 2003/09/09 20:12:37 lstein Exp $ # # BioPerl module for Bio::SeqFeature::Generic # # 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::SeqFeature::Generic - Generic SeqFeature =head1 SYNOPSIS $feat = new Bio::SeqFeature::Generic ( -start => 10, -end => 100, -strand => -1, -primary => 'repeat', -source_tag => 'repeatmasker', -score => 1000, -tag => { new => 1, author => 'someone', sillytag => 'this is silly!' } ); $feat = new Bio::SeqFeature::Generic ( -gff_string => $string ); # if you want explicitly GFF1 $feat = new Bio::SeqFeature::Generic ( -gff1_string => $string ); # add it to an annotated sequence $annseq->add_SeqFeature($feat); =head1 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 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 inherieted 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 SeqIO system =head1 Implemented Interfaces This class implementes the following interfaces. =over 4 =item Bio::SeqFeatureI Note that this includes implementing Bio::RangeI. =item Bio::AnnotatableI =item Bio::FeatureHolderI Features held by a feature are essentially sub-features. =back =head1 FEEDBACK =head2 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://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 AUTHOR - Ewan Birney Ewan Birney E<lt>birney@sanger.ac.ukE<gt> =head1 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 subfeatures =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::SeqFeature::Generic; use vars qw(@ISA); use strict; use Bio::Root::Root; use Bio::SeqFeatureI; use Bio::AnnotatableI; use Bio::FeatureHolderI; use Bio::Annotation::Collection; use Bio::Location::Simple; use Bio::Tools::GFF; #use Tie::IxHash; @ISA = qw(Bio::Root::Root Bio::SeqFeatureI Bio::AnnotatableI Bio::FeatureHolderI); sub new { my ( $caller, @args) = @_; my ($self) = $caller->SUPER::new(@args); $self->{'_parse_h'} = {}; $self->{'_gsf_tag_hash'} = {}; # tie %{$self->{'_gsf_tag_hash'}}, "Tie::IxHash"; # bulk-set attributes $self->set_attributes(@args); # done - we hope return $self; } =head2 set_attributes Title : set_attributes Usage : Function: Sets a whole array of parameters at once. Example : Returns : none Args : Named parameters, in the form as they would otherwise be passed to new(). Currently recognized are: -start start position -end end position -strand strand -primary primary tag -source source tag -frame frame -score score value -tag a reference to a tag/value hash -gff_string GFF v.2 string to initialize from -gff1_string GFF v.1 string to initialize from -seq_id the display name of the sequence -annotation the AnnotationCollectionI object -location the LocationI object =cut sub set_attributes { my ($self,@args) = @_; my ($start, $end, $strand, $primary_tag, $source_tag, $primary, $source, $frame, $score, $tag, $gff_string, $gff1_string, $seqname, $seqid, $annot, $location,$display_name) = $self->_rearrange([qw(START END STRAND PRIMARY_TAG SOURCE_TAG PRIMARY SOURCE FRAME SCORE TAG GFF_STRING GFF1_STRING SEQNAME SEQ_ID ANNOTATION LOCATION DISPLAY_NAME )], @args); $location && $self->location($location); $gff_string && $self->_from_gff_string($gff_string); $gff1_string && do { $self->gff_format(Bio::Tools::GFF->new('-gff_version' => 1)); $self->_from_gff_stream($gff1_string); }; $primary_tag && $self->primary_tag($primary_tag); $source_tag && $self->source_tag($source_tag); $primary && $self->primary_tag($primary); $source && $self->source_tag($source); defined $start && $self->start($start); defined $end && $self->end($end); defined $strand && $self->strand($strand); defined $frame && $self->frame($frame); $score && $self->score($score); $annot && $self->annotation($annot); defined $display_name && $self->display_name($display_name); if($seqname) { $self->warn("-seqname is deprecated. Please use -seq_id instead."); $seqid = $seqname unless $seqid; } $seqid && $self->seq_id($seqid); $tag && do { foreach my $t ( keys %$tag ) { $self->add_tag_value($t,$tag->{$t}); } }; } =head2 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 =cut sub direct_new { my ( $class) = @_; my ($self) = {}; bless $self,$class; return $self; } =head2 location Title : location Usage : my $location = $seqfeature->location() Function: returns a location object suitable for identifying location of feature on sequence or parent feature Returns : Bio::LocationI object Args : [optional] Bio::LocationI object to set the value to. =cut sub location { my($self, $value ) = @_; if (defined($value)) { unless (ref($value) and $value->isa('Bio::LocationI')) { $self->throw("object $value pretends to be a location but ". "does not implement Bio::LocationI"); } $self->{'_location'} = $value; } elsif (! $self->{'_location'}) { # guarantees a real location object is returned every time $self->{'_location'} = Bio::Location::Simple->new(); } return $self->{'_location'}; } =head2 start Title : start Usage : $start = $feat->start $feat->start(20) Function: Get/set on the start coordinate of the feature Returns : integer Args : none =cut sub start { my ($self,$value) = @_; return $self->location->start($value); } =head2 end Title : end Usage : $end = $feat->end $feat->end($end) Function: get/set on the end coordinate of the feature Returns : integer Args : none =cut sub end { my ($self,$value) = @_; return $self->location->end($value); } =head2 length Title : length Usage : Function: Example : Returns : Args : =cut sub length { my ($self) = @_; return $self->end - $self->start() + 1; } =head2 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 =cut sub strand { my ($self,$value) = @_; return $self->location->strand($value); } =head2 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 =cut sub score { my ($self,$value) = @_; if (defined($value)) { if ( $value !~ /^[+-]?\d+\.?\d*(e-\d+)?/ ) { $self->throw("'$value' is not a valid score"); } $self->{'_gsf_score'} = $value; } return $self->{'_gsf_score'}; } =head2 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 =cut sub frame { my ($self,$value) = @_; if ( defined $value ) { if ( $value !~ /^[0-2.]$/ ) { $self->throw("'$value' is not a valid frame"); } if( $value eq '.' ) { $value = '.'; } $self->{'_gsf_frame'} = $value; } return $self->{'_gsf_frame'}; } =head2 primary_tag Title : primary_tag Usage : $tag = $feat->primary_tag() $feat->primary_tag('exon') Function: get/set on the primary tag for a feature, eg 'exon' Returns : a string Args : none =cut sub primary_tag { my ($self,$value) = @_; if ( defined $value ) { $self->{'_primary_tag'} = $value; } return $self->{'_primary_tag'}; } =head2 source_tag Title : source_tag Usage : $tag = $feat->source_tag() $feat->source_tag('genscan'); Function: Returns the source tag for a feature, eg, 'genscan' Returns : a string Args : none =cut sub source_tag { my ($self,$value) = @_; if( defined $value ) { $self->{'_source_tag'} = $value; } return $self->{'_source_tag'}; } =head2 has_tag Title : has_tag Usage : $value = $self->has_tag('some_tag') Function: Tests wether a feature contaings a tag Returns : TRUE if the SeqFeature has the tag, and FALSE otherwise. Args : The name of a tag =cut sub has_tag { my ($self, $tag) = @_; return exists $self->{'_gsf_tag_hash'}->{$tag}; } =head2 add_tag_value Title : add_tag_value Usage : $self->add_tag_value('note',"this is a note"); Returns : TRUE on success Args : tag (string) and value (any scalar) =cut sub add_tag_value { my ($self, $tag, $value) = @_; $self->{'_gsf_tag_hash'}->{$tag} ||= []; push(@{$self->{'_gsf_tag_hash'}->{$tag}},$value); } =head2 get_tag_values Title : get_tag_values Usage : @values = $gsf->get_tag_values('note'); Function: Returns a list of all the values stored under a particular tag. Returns : A list of scalars Args : The name of the tag =cut sub get_tag_values { my ($self, $tag) = @_; if( ! defined $tag ) { return (); } if ( ! exists $self->{'_gsf_tag_hash'}->{$tag} ) { $self->throw("asking for tag value that does not exist $tag"); } return @{$self->{'_gsf_tag_hash'}->{$tag}}; } =head2 get_all_tags Title : get_all_tags Usage : @tags = $feat->get_all_tags() Function: Get a list of all the tags in a feature Returns : An array of tag names Args : none =cut sub get_all_tags { my ($self, @args) = @_; return keys %{ $self->{'_gsf_tag_hash'}}; } =head2 remove_tag Title : remove_tag Usage : $feat->remove_tag('some_tag') Function: removes a tag from this feature Returns : the array of values for this tag before removing it Args : tag (string) =cut sub remove_tag { my ($self, $tag) = @_; if ( ! exists $self->{'_gsf_tag_hash'}->{$tag} ) { $self->throw("trying to remove a tag that does not exist: $tag"); } my @vals = @{$self->{'_gsf_tag_hash'}->{$tag}}; delete $self->{'_gsf_tag_hash'}->{$tag}; return @vals; } =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 Example : Returns : TRUE on success Args : a Bio::PrimarySeqI compliant object =cut sub attach_seq { my ($self, $seq) = @_; if ( ! ($seq && ref($seq) && $seq->isa("Bio::PrimarySeqI")) ) { $self->throw("Must attach Bio::PrimarySeqI objects to SeqFeatures"); } $self->{'_gsf_seq'} = $seq; # attach to sub features if they want it foreach ( $self->sub_SeqFeature() ) { $_->attach_seq($seq); } return 1; } =head2 seq Title : seq Usage : $tseq = $sf->seq() Function: returns the truncated sequence (if there) for this Example : Returns : sub seq (a Bio::PrimarySeqI compliant object) on attached sequence bounded by start & end, or undef if there is no sequence attached Args : none =cut sub seq { my ($self, $arg) = @_; if ( defined $arg ) { $self->throw("Calling SeqFeature::Generic->seq with an argument. You probably want attach_seq"); } if ( ! exists $self->{'_gsf_seq'} ) { return undef; } # assumming our seq object is sensible, it should not have to yank # the entire sequence out here. my $seq = $self->{'_gsf_seq'}->trunc($self->start(), $self->end()); if ( $self->strand == -1 ) { # ok. this does not work well (?) #print STDERR "Before revcom", $seq->str, "\n"; $seq = $seq->revcom; #print STDERR "After revcom", $seq->str, "\n"; } return $seq; } =head2 entire_seq Title : entire_seq Usage : $whole_seq = $sf->entire_seq() Function: gives the entire sequence that this seqfeature is attached to Example : Returns : a Bio::PrimarySeqI compliant object, or undef if there is no sequence attached Args : =cut sub entire_seq { my ($self) = @_; return $self->{'_gsf_seq'}; } =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 { my ($obj,$value) = @_; if ( defined $value ) { $obj->{'_gsf_seq_id'} = $value; } return $obj->{'_gsf_seq_id'}; } =head2 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 =cut sub display_name{ my $self = shift; return $self->{'display_name'} = shift if @_; return $self->{'display_name'}; } =head1 Methods for implementing Bio::AnnotatableI =cut =head2 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) =cut sub annotation { my ($obj,$value) = @_; # we are smart if someone references the object and there hasn't been # one set yet if(defined $value || ! defined $obj->{'annotation'} ) { $value = new Bio::Annotation::Collection unless ( defined $value ); $obj->{'annotation'} = $value; } return $obj->{'annotation'}; } =head1 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. =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) = @_; if ($self->{'_gsf_sub_array'}) { return @{$self->{'_gsf_sub_array'}}; } else { return; } } =head2 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 =cut #' sub add_SeqFeature{ my ($self,$feat,$expand) = @_; if ( !$feat->isa('Bio::SeqFeatureI') ) { $self->warn("$feat does not implement Bio::SeqFeatureI. Will add it anyway, but beware..."); } if($expand && ($expand eq 'EXPAND')) { $self->_expand_region($feat); } else { if ( !$self->contains($feat) ) { $self->throw("$feat is not contained within parent feature, and expansion is not valid"); } } $self->{'_gsf_sub_array'} = [] unless exists($self->{'_gsf_sub_array'}); push(@{$self->{'_gsf_sub_array'}},$feat); } =head2 remove_SeqFeatures Title : remove_SeqFeatures Usage : $sf->remove_SeqFeatures Function: Removes all sub SeqFeatures If you want to remove only a subset, remove that subset from the returned array, and add back the rest. Example : Returns : The array of Bio::SeqFeatureI implementing sub-features that was deleted from this feature. Args : none =cut sub remove_SeqFeatures { my ($self) = @_; my @subfeats = @{$self->{'_gsf_sub_array'}}; $self->{'_gsf_sub_array'} = []; # zap the array implicitly. return @subfeats; } =head1 GFF-related methods =cut =head2 gff_format Title : gff_format Usage : # get: $gffio = $feature->gff_format(); # set (change the default version of GFF2): $feature->gff_format(Bio::Tools::GFF->new(-gff_version => 1)); Function: Get/set the GFF format interpreter. This object is supposed to format and parse GFF. See Bio::Tools::GFF for the interface. If this method is called as class method, the default for all newly created instances will be changed. Otherwise only this instance will be affected. Example : Returns : a Bio::Tools::GFF compliant object Args : On set, an instance of Bio::Tools::GFF or a derived object. =cut sub gff_format { my ($self, $gffio) = @_; if(defined($gffio)) { if(ref($self)) { $self->{'_gffio'} = $gffio; } else { $Bio::SeqFeatureI::static_gff_formatter = $gffio; } } return (ref($self) && exists($self->{'_gffio'}) ? $self->{'_gffio'} : $self->_static_gff_formatter); } =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. 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(). =cut sub gff_string{ my ($self,$formatter) = @_; $formatter = $self->gff_format() unless $formatter; return $formatter->gff_string($self); } # =head2 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 : # # =cut sub slurp_gff_file { my ($f) = @_; my @out; if ( !defined $f ) { die "Must have a filehandle"; } Bio::Root::Root->warn("deprecated method slurp_gff_file() called in Bio::SeqFeature::Generic. Use Bio::Tools::GFF instead."); while(<$f>) { my $sf = Bio::SeqFeature::Generic->new('-gff_string' => $_); push(@out, $sf); } return @out; } =head2 _from_gff_string Title : _from_gff_string Usage : Function: Set feature properties from GFF string. This method uses the object returned by gff_format() for the actual interpretation of the string. Set a different GFF format interpreter first if you need a specific version, like GFF1. (The default is GFF2.) Example : Returns : Args : a GFF-formatted string =cut sub _from_gff_string { my ($self, $string) = @_; $self->gff_format()->from_gff_string($self, $string); } =head2 _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. =cut sub _expand_region { my ($self, $feat) = @_; if(! $feat->isa('Bio::SeqFeatureI')) { $self->warn("$feat does not implement Bio::SeqFeatureI"); } # if this doesn't have start/end set - forget it! if((! defined($self->start())) && (! defined $self->end())) { $self->start($feat->start()); $self->end($feat->end()); $self->strand($feat->strand) unless defined($self->strand()); } else { my $range = $self->union($feat); $self->start($range->start); $self->end($range->end); $self->strand($range->strand); } } =head2 _parse Title : _parse Usage : Function: Parsing hints Example : Returns : Args : =cut sub _parse { my ($self) = @_; return $self->{'_parse_h'}; } =head2 _tag_value Title : _tag_value Usage : Function: For internal use only. Convenience method for those tags that may only have a single value. Returns : Args : =cut sub _tag_value { my ($self, $tag, $value) = @_; if(defined($value) || (! $self->has_tag($tag))) { $self->remove_tag($tag) if($self->has_tag($tag)); $self->add_tag_value($tag, $value); } return ($self->each_tag_value($tag))[0]; } ####################################################################### # aliases for methods that changed their names in an attempt to make # # bioperl names more consistent # ####################################################################### sub seqname { my $self = shift; $self->warn("SeqFeatureI::seqname() is deprecated. Please use seq_id() instead."); return $self->seq_id(@_); } sub display_id { my $self = shift; $self->warn("SeqFeatureI::display_id() is deprecated. Please use display_name() instead."); return $self->display_name(@_); } # this is towards consistent naming sub each_tag_value { return shift->get_tag_values(@_); } sub all_tags { return shift->get_all_tags(@_); } # we revamped the feature containing property to implementing # Bio::FeatureHolderI *sub_SeqFeature = \&get_SeqFeatures; *add_sub_SeqFeature = \&add_SeqFeature; *flush_sub_SeqFeatures = \&remove_SeqFeatures; # this one is because of inconsistent naming ... *flush_sub_SeqFeature = \&remove_SeqFeatures; 1;