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# $Id: MZEF.pm,v 1.7 2001/05/16 14:57:44 heikki Exp $
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# BioPerl module for Bio::Tools::MZEF
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# Cared for by Hilmar Lapp <hlapp@gmx.net>
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# Copyright Hilmar Lapp
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# You may distribute this module under the same terms as perl itself
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# POD documentation - main docs before the code
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Bio::Tools::MZEF - Results of one MZEF run
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$mzef = Bio::Tools::MZEF->new(-file => 'result.mzef');
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$mzef = Bio::Tools::MZEF->new( -fh => \*INPUT );
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# to indicate that the sequence was reversed prior to feeding it to MZEF
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# and that you want to have this reflected in the strand() attribute of
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# the exons, as well have the coordinates translated to the non-reversed
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$mzef = Bio::Tools::MZEF->new( -file => 'result.mzef',
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# note: this class is-a Bio::Tools::AnalysisResult which implements
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# Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same
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while($gene = $mzef->next_prediction()) {
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# $gene is an instance of Bio::Tools::Prediction::Gene
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# $gene->exons() returns an array of
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# Bio::Tools::Prediction::Exon objects
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@exon_arr = $gene->exons();
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@intrl_exons = $gene->exons('Internal');
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# note that presently MZEF predicts only internal exons!
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# essential if you gave a filename at initialization (otherwise the file
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The MZEF module provides a parser for MZEF gene structure prediction
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This module inherits off L<Bio::Tools::AnalysisResult> and therefore
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implements L<Bio::SeqAnalysisParserI>.
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User feedback is an integral part of the evolution of this and other
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Bioperl modules. Send your comments and suggestions preferably to one
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of the Bioperl mailing lists. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bio.perl.org/MailList.html - About the mailing lists
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Report bugs to the Bioperl bug tracking system to help us keep track
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the bugs and their resolution. Bug reports can be submitted via email
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bioperl-bugs@bio.perl.org
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http://bio.perl.org/bioperl-bugs/
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=head1 AUTHOR - Hilmar Lapp
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Email hlapp@gmx.net (or hilmar.lapp@pharma.novartis.com)
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Describe contact details here
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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# Let the code begin...
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package Bio::Tools::MZEF;
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use Bio::Tools::AnalysisResult;
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use Bio::Tools::Prediction::Gene;
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use Bio::Tools::Prediction::Exon;
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@ISA = qw(Bio::Tools::AnalysisResult);
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sub _initialize_state {
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my($self,@args) = @_;
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# first call the inherited method!
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my $make = $self->SUPER::_initialize_state(@args);
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# handle our own parameters
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my ($strand, $params) =
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$self->_rearrange([qw(STRAND
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# our private state variables
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$strand = 1 unless defined($strand);
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$self->{'_strand'} = $strand;
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$self->{'_preds_parsed'} = 0;
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$self->{'_has_cds'} = 0;
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# array of pre-parsed predictions
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$self->{'_preds'} = [];
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=head2 analysis_method
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Usage : $mzef->analysis_method();
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Purpose : Inherited method. Overridden to ensure that the name matches
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sub analysis_method {
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my ($self, $method) = @_;
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if($method && ($method !~ /mzef/i)) {
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$self->throw("method $method not supported in " . ref($self));
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return $self->SUPER::analysis_method($method);
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Usage : while($gene = $mzef->next_feature()) {
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Function: Returns the next gene structure prediction of the MZEF result
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file. Call this method repeatedly until FALSE is returned.
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The returned object is actually a SeqFeatureI implementing object.
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This method is required for classes implementing the
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SeqAnalysisParserI interface, and is merely an alias for
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next_prediction() at present.
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Note that with the present version of MZEF there will only be one
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object returned, because MZEF does not predict individual genes
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but just potential internal exons.
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Returns : A Bio::Tools::Prediction::Gene object.
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my ($self,@args) = @_;
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# even though next_prediction doesn't expect any args (and this method
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# does neither), we pass on args in order to be prepared if this changes
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return $self->next_prediction(@args);
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=head2 next_prediction
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Title : next_prediction
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Usage : while($gene = $mzef->next_prediction()) {
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Function: Returns the next gene structure prediction of the MZEF result
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file. Call this method repeatedly until FALSE is returned.
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Note that with the present version of MZEF there will only be one
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object returned, because MZEF does not predict individual genes
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but just potential internal exons.
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Returns : A Bio::Tools::Prediction::Gene object.
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sub next_prediction {
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# if the prediction section hasn't been parsed yet, we do this now
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$self->_parse_predictions() unless $self->_predictions_parsed();
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# return the next gene structure (transcript)
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return $self->_prediction();
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=head2 _parse_predictions
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Title : _parse_predictions()
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Usage : $obj->_parse_predictions()
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Function: Parses the prediction section. Automatically called by
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next_prediction() if not yet done.
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sub _parse_predictions {
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my ($method); # set but not used presently
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my $exon_tag = "InternalExon";
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# my $seqname; # name given in output is poorly formatted
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while(defined($_ = $self->_readline())) {
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if(/^\s*(\d+)\s*-\s*(\d+)\s+/) {
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if(! defined($gene)) {
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$gene = Bio::Tools::Prediction::Gene->new(
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'-primary' => "GenePrediction$prednr",
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'-source' => 'MZEF');
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# we handle start-end first because may not be space delimited
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my ($start,$end) = ($1,$2);
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s/^\s*(\d+)\s*-\s*(\d+)\s+//;
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# split the rest into fields
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# format: Coordinates P Fr1 Fr2 Fr3 Orf 3ss Cds 5ss
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# index: 0 1 2 3 4 5 6 7
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my @flds = split(' ', $_);
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# create the feature object depending on the type of signal --
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# which is always an (internal) exon for MZEF
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my $predobj = Bio::Tools::Prediction::Exon->new();
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$predobj->source_tag('MZEF');
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$predobj->significance($flds[0]);
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$predobj->score($flds[0]); # what shall we set as overall score?
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$predobj->strand($self->{'_strand'}); # MZEF searches only one
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if($predobj->strand() == 1) {
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$predobj->start($start);
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$predobj->start($seqlen-$end+1);
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$predobj->end($seqlen-$start+1);
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$predobj->start_signal_score($flds[5]);
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$predobj->end_signal_score($flds[7]);
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$predobj->coding_signal_score($flds[6]);
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# frame -- we simply extract the one with highest score from the
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# orf field, and store the individual scores for now
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my $frm = index($flds[4], "1");
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$predobj->frame(($frm < 0) ? undef : $frm);
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$predobj->primary_tag($exon_tag);
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$predobj->is_coding(1);
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# add to gene structure (should be done only when start and end
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# are set, in order to allow for proper expansion of the range)
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$gene->add_exon($predobj);
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if(/^\s*Internal .*(MZEF)/) {
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$self->analysis_method($1);
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if(/^\s*File_Name:\s+(\S+)\s+Sequence_length:\s+(\d+)/) {
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# $seqname = $1; # this is too poor currently (file name truncated
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# to 10 chars) in order to be sensible enough
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# $gene->seqname($seqname);
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$self->_add_prediction($gene) if defined($gene);
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$self->_predictions_parsed(1);
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Title : _prediction()
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Usage : $gene = $obj->_prediction()
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return undef unless(exists($self->{'_preds'}) && @{$self->{'_preds'}});
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return shift(@{$self->{'_preds'}});
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=head2 _add_prediction
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Title : _add_prediction()
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Usage : $obj->_add_prediction($gene)
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sub _add_prediction {
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my ($self, $gene) = @_;
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if(! exists($self->{'_preds'})) {
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$self->{'_preds'} = [];
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push(@{$self->{'_preds'}}, $gene);
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=head2 _predictions_parsed
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Title : _predictions_parsed
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Usage : $obj->_predictions_parsed
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Returns : TRUE or FALSE
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sub _predictions_parsed {
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my ($self, $val) = @_;
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$self->{'_preds_parsed'} = $val if $val;
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if(! exists($self->{'_preds_parsed'})) {
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$self->{'_preds_parsed'} = 0;
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return $self->{'_preds_parsed'};
added
removed
Bio/Tools/MZEF.pm
