Raw content of Bio::Tools::MZEF # $Id: MZEF.pm,v 1.9 2002/10/22 07:38:46 lapp Exp $ # # BioPerl module for Bio::Tools::MZEF # # Cared for by Hilmar Lapp <hlapp@gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::MZEF - Results of one MZEF run =head1 SYNOPSIS $mzef = Bio::Tools::MZEF->new(-file => 'result.mzef'); # filehandle: $mzef = Bio::Tools::MZEF->new( -fh => \*INPUT ); # to indicate that the sequence was reversed prior to feeding it to MZEF # and that you want to have this reflected in the strand() attribute of # the exons, as well have the coordinates translated to the non-reversed # sequence $mzef = Bio::Tools::MZEF->new( -file => 'result.mzef', -strand => -1 ); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same while($gene = $mzef->next_prediction()) { # $gene is an instance of Bio::Tools::Prediction::Gene # $gene->exons() returns an array of # Bio::Tools::Prediction::Exon objects # all exons: @exon_arr = $gene->exons(); # internal exons only @intrl_exons = $gene->exons('Internal'); # note that presently MZEF predicts only internal exons! } # essential if you gave a filename at initialization (otherwise the file # will stay open) $mzef->close(); =head1 DESCRIPTION The MZEF module provides a parser for MZEF gene structure prediction output. This module inherits off L<Bio::Tools::AnalysisResult> and therefore implements L<Bio::SeqAnalysisParserI>. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Hilmar Lapp Email hlapp@gmx.net (or hilmar.lapp@pharma.novartis.com) Describe contact details here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::MZEF; use vars qw(@ISA); use strict; use Bio::Tools::AnalysisResult; use Bio::Tools::Prediction::Gene; use Bio::Tools::Prediction::Exon; @ISA = qw(Bio::Tools::AnalysisResult); sub _initialize_state { my($self,@args) = @_; # first call the inherited method! my $make = $self->SUPER::_initialize_state(@args); # handle our own parameters my ($strand, $params) = $self->_rearrange([qw(STRAND )], @args); # our private state variables $strand = 1 unless defined($strand); $self->{'_strand'} = $strand; $self->{'_preds_parsed'} = 0; $self->{'_has_cds'} = 0; # array of pre-parsed predictions $self->{'_preds'} = []; } =head2 analysis_method Usage : $mzef->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /mzef/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /mzef/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 next_feature Title : next_feature Usage : while($gene = $mzef->next_feature()) { # do something } Function: Returns the next gene structure prediction of the MZEF result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_feature { my ($self,@args) = @_; # even though next_prediction doesn't expect any args (and this method # does neither), we pass on args in order to be prepared if this changes # ever return $self->next_prediction(@args); } =head2 next_prediction Title : next_prediction Usage : while($gene = $mzef->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the MZEF result file. Call this method repeatedly until FALSE is returned. Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_prediction { my ($self) = @_; my $gene; # if the prediction section hasn't been parsed yet, we do this now $self->_parse_predictions() unless $self->_predictions_parsed(); # return the next gene structure (transcript) return $self->_prediction(); } =head2 _parse_predictions Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : =cut sub _parse_predictions { my ($self) = @_; my ($method); # set but not used presently my $exon_tag = "InternalExon"; my $gene; # my $seqname; # name given in output is poorly formatted my $seqlen; my $prednr = 1; while(defined($_ = $self->_readline())) { if(/^\s*(\d+)\s*-\s*(\d+)\s+/) { # exon or signal if(! defined($gene)) { $gene = Bio::Tools::Prediction::Gene->new( '-primary' => "GenePrediction$prednr", '-source' => 'MZEF'); } # we handle start-end first because may not be space delimited # for large numbers my ($start,$end) = ($1,$2); s/^\s*(\d+)\s*-\s*(\d+)\s+//; # split the rest into fields chomp(); # format: Coordinates P Fr1 Fr2 Fr3 Orf 3ss Cds 5ss # index: 0 1 2 3 4 5 6 7 my @flds = split(' ', $_); # create the feature object depending on the type of signal -- # which is always an (internal) exon for MZEF my $predobj = Bio::Tools::Prediction::Exon->new(); # set common fields $predobj->source_tag('MZEF'); $predobj->significance($flds[0]); $predobj->score($flds[0]); # what shall we set as overall score? $predobj->strand($self->{'_strand'}); # MZEF searches only one if($predobj->strand() == 1) { $predobj->start($start); $predobj->end($end); } else { $predobj->start($seqlen-$end+1); $predobj->end($seqlen-$start+1); } # set scores $predobj->start_signal_score($flds[5]); $predobj->end_signal_score($flds[7]); $predobj->coding_signal_score($flds[6]); # frame -- we simply extract the one with highest score from the # orf field, and store the individual scores for now my $frm = index($flds[4], "1"); $predobj->frame(($frm < 0) ? undef : $frm); $predobj->primary_tag($exon_tag); $predobj->is_coding(1); # add to gene structure (should be done only when start and end # are set, in order to allow for proper expansion of the range) $gene->add_exon($predobj); next; } if(/^\s*Internal .*(MZEF)/) { $self->analysis_method($1); next; } if(/^\s*File_Name:\s+(\S+)\s+Sequence_length:\s+(\d+)/) { # $seqname = $1; # this is too poor currently (file name truncated # to 10 chars) in order to be sensible enough $seqlen = $2; next; } } # $gene->seq_id($seqname); $self->_add_prediction($gene) if defined($gene); $self->_predictions_parsed(1); } =head2 _prediction Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : =cut sub _prediction { my ($self) = @_; return undef unless(exists($self->{'_preds'}) && @{$self->{'_preds'}}); return shift(@{$self->{'_preds'}}); } =head2 _add_prediction Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns : =cut sub _add_prediction { my ($self, $gene) = @_; if(! exists($self->{'_preds'})) { $self->{'_preds'} = []; } push(@{$self->{'_preds'}}, $gene); } =head2 _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE =cut sub _predictions_parsed { my ($self, $val) = @_; $self->{'_preds_parsed'} = $val if $val; if(! exists($self->{'_preds_parsed'})) { $self->{'_preds_parsed'} = 0; } return $self->{'_preds_parsed'}; } 1;