Bio::SeqFeature::Gene Transcript
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Summary
Bio::SeqFeature::Gene::Transcript - A feature representing a transcript
Package variables
No package variables defined.
Included modules
Bio::PrimarySeq
Inherit
Bio::SeqFeature::Gene::TranscriptI Bio::SeqFeature::Generic
Synopsis
  # See documentation of methods.
Description
A feature representing a transcript.
Methods
new
No description
Code
promotersDescriptionCode
add_promoterDescriptionCode
flush_promotersDescriptionCode
exonsDescriptionCode
exons_orderedDescriptionCode
add_exonDescriptionCode
flush_exonsDescriptionCode
intronsDescriptionCode
poly_A_siteDescriptionCode
utrsDescriptionCode
add_utrDescriptionCode
flush_utrsDescriptionCode
sub_SeqFeatureDescriptionCode
flush_sub_SeqFeatureDescriptionCode
cdsDescriptionCode
proteinDescriptionCode
mrnaDescriptionCode
_get_typed_keys
No description
Code
_make_cds
No description
Code
featuresDescriptionCode
features_orderedDescriptionCode
get_unordered_feature_type
No description
Code
get_feature_type
No description
Code
_flush
No description
Code
_add
No description
Code
_stranded_sort
No description
Code
_new_of_type
No description
Code
transcript_destroy
No description
Code
Methods description
promoterscode    nextTop
 Title   : promoters()
Usage : @proms = $transcript->promoters();
Function: Get the promoter features/sites of this transcript.
Note that OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it. Returns : An array of Bio::SeqFeatureI implementing objects representing the promoter regions or sites. Args :
add_promotercodeprevnextTop
 Title   : add_promoter()
Usage : $transcript->add_promoter($feature);
Function: Add a promoter feature/site to this transcript.
Note that OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it. Returns : Args : A Bio::SeqFeatureI implementing object.
flush_promoterscodeprevnextTop
 Title   : flush_promoters()
Usage : $transcript->flush_promoters();
Function: Remove all promoter features/sites from this transcript.
Note that OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it. Returns : the removed features as a list Args : none
exonscodeprevnextTop
 Title   : exons()
Usage : @exons = $gene->exons();
($inital_exon) = $gene->exons('Initial');
Function: Get all exon features or all exons of specified type of this
transcript.
Exon type is treated as a case-insensitive regular expression and is optional. For consistency, use only the following types: initial, internal, terminal. Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects. Args : An optional string specifying the primary_tag of the feature.
exons_orderedcodeprevnextTop
 Title   : exons_ordered
Usage : @exons = $gene->exons_ordered();
@exons = $gene->exons_ordered("Internal");
Function: Get an ordered list of all exon features or all exons of specified
type of this transcript.
Exon type is treated as a case-insensitive regular expression and is optional. For consistency, use only the following types: Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects. Args : An optional string specifying the primary_tag of the feature.
add_exoncodeprevnextTop
 Title   : add_exon()
Usage : $transcript->add_exon($exon,'initial');
Function: Add a exon feature to this transcript.
The second argument denotes the type of exon. Mixing exons with and without a type is likely to cause trouble in exons(). Either leave out the type for all exons or for none. Presently, the following types are known: initial, internal, terminal, utr, utr5prime, and utr3prime (all case-insensitive). UTR should better be added through utrs()/add_utr(). If you wish to use other or additional types, you will almost certainly have to call exon_type_sortorder() in order to replace the default sort order, or mrna(), cds(), protein(), and exons() may yield unexpected results. Returns : Args : A Bio::SeqFeature::Gene::ExonI implementing object. A string indicating the type of the exon (optional).
flush_exonscodeprevnextTop
 Title   : flush_exons()
Usage : $transcript->flush_exons();
$transcript->flush_exons('terminal');
Function: Remove all or a certain type of exon features from this transcript.
See add_exon() for documentation about types. Calling without a type will not flush UTRs. Call flush_utrs() for this purpose. Returns : the deleted features as a list Args : A string indicating the type of the exon (optional).
intronscodeprevnextTop
 Title   : introns()
Usage : @introns = $gene->introns();
Function: Get all intron features this gene structure.
Note that this implementation generates these features on-the-fly, that is, it simply treats all regions between exons as introns, assuming that exons do not overlap. A consequence is that a consistent correspondence between the elements in the returned array and the array that exons() returns will exist only if the exons are properly sorted within their types (forward for plus- strand and reverse for minus-strand transcripts). To ensure correctness the elements in the array returned will always be sorted. Returns : An array of Bio::SeqFeature::Gene::Intron objects representing the intron regions. Args :
poly_A_sitecodeprevnextTop
 Title   : poly_A_site()
Usage : $polyAsite = $transcript->poly_A_site();
Function: Get/set the poly-adenylation feature/site of this transcript.
Returns : A Bio::SeqFeatureI implementing object representing the
poly-adenylation region.
Args : A Bio::SeqFeatureI implementing object on set, or FALSE to flush
a previously set object.
utrscodeprevnextTop
 Title   : utrs()
Usage : @utr_sites = $transcript->utrs('utr3prime');
@utr_sites = $transcript->utrs('utr5prime');
@utr_sites = $transcript->utrs();
Function: Get the features representing untranslated regions (UTR) of this
transcript.
You may provide an argument specifying the type of UTR. Currently the following types are recognized: utr5prime utr3prime for UTR on the 5' and 3' end of the CDS, respectively. Returns : An array of Bio::SeqFeature::Gene::UTR objects representing the UTR regions or sites. Args : Optionally, either utr3prime, or utr5prime for the the type of UTR feature.
add_utrcodeprevnextTop
 Title   : add_utr()
Usage : $transcript->add_utr($utrobj, 'utr3prime');
$transcript->add_utr($utrobj);
Function: Add a UTR feature/site to this transcript.
The second parameter is optional and denotes the type of the UTR feature. Presently recognized types include 'utr5prime' and 'utr3prime' for UTR on the 5' and 3' end of a gene, respectively. Calling this method is the same as calling add_exon($utrobj, 'utr'.$type). In this sense a UTR object is a special exon object, which is transcribed, not spliced out, but not translated. Note that the object supplied should return FALSE for is_coding(). Otherwise cds() and friends will become confused. Returns : Args : A Bio::SeqFeature::Gene::UTR implementing object.
flush_utrscodeprevnextTop
 Title   : flush_utrs()
Usage : $transcript->flush_utrs();
$transcript->flush_utrs('utr3prime');
Function: Remove all or a specific type of UTR features/sites from this
transcript.
Cf. add_utr() for documentation about recognized types. Returns : a list of the removed features Args : Optionally a string denoting the type of UTR feature.
sub_SeqFeaturecodeprevnextTop
 Title   : sub_SeqFeature
Usage : @feats = $transcript->sub_SeqFeature();
Function: Returns an array of all subfeatures.
This method is defined in Bio::SeqFeatureI. We override this here to include the exon etc features. Returns : An array Bio::SeqFeatureI implementing objects. Args : none
flush_sub_SeqFeaturecodeprevnextTop
 Title   : flush_sub_SeqFeature
Usage : $transcript->flush_sub_SeqFeature();
$transcript->flush_sub_SeqFeature(1);
Function: Removes all subfeatures.
This method is overridden from Bio::SeqFeature::Generic to flush all additional subfeatures like exons, promoters, etc., which is almost certainly not what you want. To remove only features added through $transcript->add_sub_SeqFeature($feature) pass any argument evaluating to TRUE. Example : Returns : none Args : Optionally, an argument evaluating to TRUE will suppress flushing of all transcript-specific subfeatures (exons etc.).
cdscodeprevnextTop
 Title   : cds
Usage : $seq = $transcript->cds();
Function: Returns the CDS (coding sequence) as defined by the exons
of this transcript and the attached sequence.
If no sequence is attached this method will return false. Note that the implementation provided here returns a concatenation of all coding exons, thereby assuming that exons do not overlap. Note also that you cannot set the CDS via this method. Set a single CDS feature as a single exon, or derive your own class if you want to store a predicted CDS. Example : Returns : A Bio::PrimarySeqI implementing object. Args :
proteincodeprevnextTop
 Title   : protein()
Usage : $protein = $transcript->protein();
Function: Get the protein encoded by the transcript as a sequence object.
The implementation provided here simply calls translate() on the object returned by cds(). Returns : A Bio::PrimarySeqI implementing object. Args :
mrnacodeprevnextTop
 Title   : mrna()
Usage : $mrna = $transcript->mrna();
Function: Get the mRNA of the transcript as a sequence object.
The difference to cds() is that the sequence object returned by this methods will also include UTR and the poly-adenylation site, but not promoter sequence (TBD). HL: do we really need this method? Returns : A Bio::PrimarySeqI implementing object. Args :
featurescodeprevnextTop
 Title   : features
Usage : my @features=$transcript->features;
Function: returns all the features associated with this transcript
Returns : a list of SeqFeatureI implementing objects
Args : none
features_orderedcodeprevnextTop
 Title   : features_ordered
Usage : my @features=$transcript->features_ordered;
Function: returns all the features associated with this transcript,
in order by feature start, according to strand
Returns : a list of SeqFeatureI implementing objects
Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my ($caller, @args) = @_;
    my $self = $caller->SUPER::new(@args);
    $self->_register_for_cleanup(\&transcript_destroy);
    my ($primary) = $self->_rearrange([qw(PRIMARY)],@args);

    $primary = 'transcript' unless $primary;
    $self->primary_tag($primary);
    $self->strand(0) if(! defined($self->strand()));
    return $self;
}
promotersdescriptionprevnextTop
sub promoters {
    my ($self) = @_;
    return $self->get_feature_type('Bio::SeqFeature::Gene::Promoter');
}
add_promoterdescriptionprevnextTop
sub add_promoter {
    my ($self, $fea) = @_;
    $self->_add($fea,'Bio::SeqFeature::Gene::Promoter');
}
flush_promotersdescriptionprevnextTop
sub flush_promoters {
    my ($self) = @_;
    return $self->_flush('Bio::SeqFeature::Gene::Promoter');
}
exonsdescriptionprevnextTop
sub exons {
    my ($self, $type) = @_;
    return $self->get_unordered_feature_type('Bio::SeqFeature::Gene::ExonI', 
					     $type);
}
exons_ordereddescriptionprevnextTop
sub exons_ordered {
     my ($self,$type) = @_;
    return $self->get_feature_type('Bio::SeqFeature::Gene::ExonI', $type);
}
add_exondescriptionprevnextTop
sub add_exon {
    my ($self, $fea, $type) = @_;
    if(! $fea->isa('Bio::SeqFeature::Gene::ExonI') ) {
	$self->throw("$fea does not implement Bio::SeqFeature::Gene::ExonI");
    }
    $self->_add($fea,'Bio::SeqFeature::Gene::Exon', $type);
}
flush_exonsdescriptionprevnextTop
sub flush_exons {
    my ($self, $type) = @_;
    return $self->_flush('Bio::SeqFeature::Gene::Exon',$type);
}
intronsdescriptionprevnextTop
sub introns {
    my ($self) = @_;
    my @introns = ();
    my @exons = $self->exons();
    my ($strand, $rev_order);

    # if there's 1 or less exons we're done
return () unless($#exons > 0); # record strand and order (a minus-strand transcript is likely to have
# the exons stacked in reverse order)
foreach my $exon (@exons) { $strand = $exon->strand(); last if $strand; # we're done if we've got 1 or -1
} $rev_order = ($exons[0]->end() < $exons[1]->start() ? 0 : 1); # Make sure exons are sorted. Because we assume they don't overlap, we
# simply sort by start position.
if((! defined($strand)) || ($strand != -1) || (! $rev_order)) { # always sort forward for plus-strand transcripts, and for negative-
# strand transcripts that appear to be unsorted or forward sorted
@exons = map { $_->[0] } sort { $a->[1] <=> $b->[1] } map { [ $_, $_->start * ($_->strand || 1)] } @exons; } else { # sort in reverse order for transcripts on the negative strand and
# found to be in reverse order
@exons = map { $_->[0] } sort { $b->[1] <=> $a->[1] } map { [ $_, $_->start()] } @exons; } # loop over all intervening gaps
while ((my $exonA = shift (@exons)) &&(my $exonB = shift(@exons))){ my $intron = Bio::SeqFeature::Gene::Intron->new(-primary=>'intron'); $intron->upstream_Exon($exonA); $intron->downstream_Exon($exonB); $intron->attach_seq($self->entire_seq) if $self->entire_seq; unshift(@exons,$exonB); push @introns,$intron; } return @introns;
}
poly_A_sitedescriptionprevnextTop
sub poly_A_site {
    my ($self, $fea) = @_;
    if ($fea) {
	$self->_add($fea,'Bio::SeqFeature::Gene::Poly_A_site');
    }
    return ($self->get_feature_type('Bio::SeqFeature::Gene::Poly_A_site'))[0];
}
utrsdescriptionprevnextTop
sub utrs {
    my ($self, $type) = @_;
    return $self->get_feature_type('Bio::SeqFeature::Gene::UTR',$type);
}
add_utrdescriptionprevnextTop
sub add_utr {
    my ($self, $fea, $type) = @_;
    $self->_add($fea,'Bio::SeqFeature::Gene::UTR',$type);
}
flush_utrsdescriptionprevnextTop
sub flush_utrs {
    my ($self, $type) = @_;
    return $self->_flush('Bio::SeqFeature::Gene::UTR',$type);
}
sub_SeqFeaturedescriptionprevnextTop
sub sub_SeqFeature {
   my ($self) = @_;   
   my @feas;
   
   # get what the parent already has
@feas = $self->SUPER::sub_SeqFeature(); # add the features we have in addition
push(@feas, $self->exons()); # this includes UTR features
push(@feas, $self->promoters()); push(@feas, $self->poly_A_site()) if($self->poly_A_site()); return @feas;
}
flush_sub_SeqFeaturedescriptionprevnextTop
sub flush_sub_SeqFeature {
   my ($self,$fea_only) = @_;

   $self->SUPER::flush_sub_SeqFeature();
   if(! $fea_only) {
       $self->flush_promoters();
       $self->flush_exons();
       $self->flush_utrs();
       $self->poly_A_site(0);
   }
}
cdsdescriptionprevnextTop
sub cds {
    my ($self) = @_;
    my @exons = $self->exons_ordered();  #this is always sorted properly according to strand
my $strand; return unless(@exons); # record strand (a minus-strand transcript must have the exons sorted in
# reverse order)
foreach my $exon (@exons) { if(defined($exon->strand()) && (! $strand)) { $strand = $exon->strand(); } if($exon->strand() && (($exon->strand() * $strand) < 0)) { $self->throw("Transcript mixes coding exons on plus and minus ". "strand. This makes no sense."); } } my $cds = $self->_make_cds(@exons); return unless $cds; return Bio::PrimarySeq->new('-id' => $self->seq_id(), '-seq' => $cds, '-alphabet' => "dna");
}
proteindescriptionprevnextTop
sub protein {
    my ($self) = @_;
    my $seq;

    $seq = $self->cds();
    return $seq->translate() if $seq;
    return;
}
mrnadescriptionprevnextTop
sub mrna {
    my ($self) = @_;
    my ($seq, $mrna, $elem);

    # get the coding part
$seq = $self->cds(); if(! $seq) { $seq = Bio::PrimarySeq->new('-id' => $self->seq_id(), '-alphabet' => "rna", '-seq' => ""); } # get and add UTR sequences
$mrna = ""; foreach $elem ($self->utrs('utr5prime')) { $mrna .= $elem->seq()->seq(); } $seq->seq($mrna . $seq->seq()); $mrna = ""; foreach $elem ($self->utrs('utr3prime')) { $mrna .= $elem->seq()->seq(); } $seq->seq($seq->seq() . $mrna); if($self->poly_A_site()) { $seq->seq($seq->seq() . $self->poly_A_site()->seq()->seq()); } return if($seq->length() == 0); return $seq;
}
_get_typed_keysdescriptionprevnextTop
sub _get_typed_keys {
    my ($self, $keyprefix, $type) = @_;
    my @keys = ();
    my @feas = ();

    # make case-insensitive
$type = ($type ? lc($type) : ""); # pull out all feature types that exist and match
@keys = grep { /^_$keyprefix$type/i; } (keys(%{$self})); return @keys;
}
_make_cdsdescriptionprevnextTop
sub _make_cds {
    my ($self,@exons) = @_;
    my $cds = "";

    foreach my $exon (@exons) {
	next if((! defined($exon->seq())) || (! $exon->is_coding()));
	my $phase = length($cds) % 3;
	# let's check the simple case 
if((! defined($exon->frame())) || ($phase == $exon->frame())) { # this one fits exactly, or frame of the exon is undefined (should
# we warn about that?); we bypass the $exon->cds() here (hmm,
# not very clean style, but I don't see where this screws up)
$cds .= $exon->seq()->seq(); } else { # this one is probably from exon shuffling and needs some work
my $seq = $exon->cds(); # now $seq is guaranteed to be in frame 0
next if(! $seq); $seq = $seq->seq(); # adjustment needed?
if($phase > 0) { # how many Ns can we chop off the piece to be added?
my $n_crop = 0; if($seq =~ /^(n+)/i) { $n_crop = length($1); } if($n_crop >= $phase) { # chop off to match the phase
$seq = substr($seq, $phase); } else { # fill in Ns
$seq = ("n" x (3-$phase)) . $seq; } } $cds .= $seq; } } return $cds;
}
featuresdescriptionprevnextTop
sub features {
    my $self = shift;    
    return grep { defined } @{$self->{'_features'} || []};
}
features_ordereddescriptionprevnextTop
sub features_ordered {
   my ($self) = @_;
   return $self->_stranded_sort(@{$self->{'_features'} || []});
}
get_unordered_feature_typedescriptionprevnextTop
sub get_unordered_feature_type {
    my ($self, $type, $pri)=@_;
    my @list;
    foreach ( $self->features) {
	if ($_->isa($type)) {
	    if ($pri && $_->primary_tag !~ /$pri/i) {
		next;
	    }
	    push @list,$_;
	}
    }
    return @list;
}
get_feature_typedescriptionprevnextTop
sub get_feature_type {
    my ($self)=shift;
    return $self->_stranded_sort($self->get_unordered_feature_type(@_));
}

#This was fixed by Gene Cutler - the indexing on the list being reversed
#fixed a bad bug. Thanks Gene!
}
_flushdescriptionprevnextTop
sub _flush {
     my ($self, $type, $pri)=@_;
     my @list=$self->features;
     my @cut;
     for (reverse (0..$#list)) {
         if (defined $list[$_] &&
	     $list[$_]->isa($type)) {
             if ($pri && $list[$_]->primary_tag !~ /$pri/i) {
                 next;
             }
             push @cut, splice @list, $_, 1;  #remove the element of $type from @list
#and return each of them in @cut
} } $self->{'_features'}=\@list; return reverse @cut;
}
_adddescriptionprevnextTop
sub _add {
    my ($self, $fea, $type, $pri)=@_;
    require Bio::SeqFeature::Gene::Promoter;
    require Bio::SeqFeature::Gene::UTR;
    require Bio::SeqFeature::Gene::Exon;
    require Bio::SeqFeature::Gene::Intron;
    require Bio::SeqFeature::Gene::Poly_A_site;

    if(! $fea->isa('Bio::SeqFeatureI') ) {
	$self->throw("$fea does not implement Bio::SeqFeatureI");
    }
    if(! $fea->isa($type) || $pri) {
	$fea=$self->_new_of_type($fea,$type,$pri);
    }
    if (! $self->strand) {
	$self->strand($fea->strand);
    } else {
	if ($self->strand * $fea->strand == -1) {
	    $self->throw("$fea is on opposite strand from $self");
	}
    }

    $self->_expand_region($fea);
    if(defined($self->entire_seq()) && (! defined($fea->entire_seq())) &&
       $fea->can('attach_seq')) {
	$fea->attach_seq($self->entire_seq());
    }
    if (defined $self->parent) {
	$self->parent->_expand_region($fea);
    }
    push(@{$self->{'_features'}}, $fea);
    1;
}
_stranded_sortdescriptionprevnextTop
sub _stranded_sort {
    my ($self,@list)=@_;
    my $strand;
    foreach my $fea (@list) {
	if($fea->strand()) {
	    # defined and != 0
$strand = $fea->strand() if(! $strand); if(($fea->strand() * $strand) < 0) { $strand = undef; last; } } } if (defined $strand && $strand == - 1) { #reverse strand
return map { $_->[0] } sort {$b->[1] <=> $a->[1]} map { [$_, $_->start] } @list; } else { #undef or forward strand
return map { $_->[0] } sort {$a->[1] <=> $b->[1]} map { [$_, $_->start] } @list; }
}
_new_of_typedescriptionprevnextTop
sub _new_of_type {
    my ($self, $fea, $type, $pri)= @_;
    my $primary;
    if ($pri) {
	$primary = $pri;    #can set new primary tag if desired
} else { ($primary) = $type =~ /.*::(.+)/; #or else primary is just end of type string
} bless $fea,$type; $fea->primary_tag($primary); return $fea;
}
transcript_destroydescriptionprevnextTop
sub transcript_destroy {
    my $self = shift;    
    # We're going to be really explicit to insure memory leaks 
# don't occur
foreach my $f ( $self->features ) { $f = undef; } $self->parent(undef); } 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
Support Top
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 - Hilmar LappTop
Email hlapp@gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _