Bio::Tools Genemark
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Summary
Bio::Tools::Genemark - Results of one Genemark run
Package variables
No package variables defined.
Included modules
Bio::Factory::FTLocationFactory
Bio::Root::Root
Bio::Seq
Bio::Tools::Prediction::Exon
Bio::Tools::Prediction::Gene
Symbol
Inherit
Bio::Tools::AnalysisResult
Synopsis
   $Genemark = Bio::Tools::Genemark->new(-file => 'result.Genemark');
# filehandle:
$Genemark = Bio::Tools::Genemark->new( -fh => \*INPUT );
# parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $Genemark->next_feature() is the same while($gene = $Genemark->next_prediction()) { # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits # off Bio::SeqFeature::Gene::Transcript. # # $gene->exons() returns an array of # Bio::Tools::Prediction::Exon objects # all exons: @exon_arr = $gene->exons(); # initial exons only @init_exons = $gene->exons('Initial'); # internal exons only @intrl_exons = $gene->exons('Internal'); # terminal exons only @term_exons = $gene->exons('Terminal'); # singleton exons: ($single_exon) = $gene->exons(); } # essential if you gave a filename at initialization (otherwise the file # will stay open) $Genemark->close();
Description
The Genemark module provides a parser for Genemark gene structure
prediction output. It parses one gene prediction into a
Bio::SeqFeature::Gene::Transcript- derived object.
This module has been developed around genemark.hmm for eukaryots v2.2a
and will probably not work with other versions.
This module also implements the Bio::SeqAnalysisParserI interface, and
thus can be used wherever such an object fits. See
Bio::SeqAnalysisParserI.
Methods
newDescriptionCode
_initialize_state
No description
Code
analysis_methodDescriptionCode
next_featureDescriptionCode
next_predictionDescriptionCode
_parse_predictionsDescriptionCode
_predictionDescriptionCode
_add_predictionDescriptionCode
_predictions_parsedDescriptionCode
_has_cdsDescriptionCode
_read_fasta_seqDescriptionCode
_seqnameDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Tools::Genemark->new();
Function: Builds a new Bio::Tools::Genemark object
Returns : an instance of Bio::Tools::Genemark
Args : seqname
analysis_methodcodeprevnextTop
 Usage     : $Genemark->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/GeneMark.hmm/i.
Returns : String
Argument : n/a
next_featurecodeprevnextTop
 Title   : next_feature
Usage : while($gene = $Genemark->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the Genemark result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Example : Returns : A Bio::Tools::Prediction::Gene object. Args :
next_predictioncodeprevnextTop
 Title   : next_prediction
Usage : while($gene = $Genemark->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the Genemark result
file. Call this method repeatedly until FALSE is returned.
Example : Returns : A Bio::Tools::Prediction::Gene object. Args :
_parse_predictionscodeprevnextTop
 Title   : _parse_predictions()
Usage : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
_predictioncodeprevnextTop
 Title   : _prediction()
Usage : $gene = $obj->_prediction()
Function: internal
Example :
Returns :
_add_predictioncodeprevnextTop
 Title   : _add_prediction()
Usage : $obj->_add_prediction($gene)
Function: internal
Example :
Returns :
_predictions_parsedcodeprevnextTop
 Title   : _predictions_parsed
Usage : $obj->_predictions_parsed
Function: internal
Example :
Returns : TRUE or FALSE
_has_cdscodeprevnextTop
 Title   : _has_cds()
Usage : $obj->_has_cds()
Function: Whether or not the result contains the predicted CDSs, too.
Example :
Returns : TRUE or FALSE
_read_fasta_seqcodeprevnextTop
 Title   : _read_fasta_seq()
Usage : ($id,$seqstr) = $obj->_read_fasta_seq();
Function: Simple but specialised FASTA format sequence reader. Uses
$self->_readline() to retrieve input, and is able to strip off
the traling description lines.
Example :
Returns : An array of two elements.
_seqnamecodeprevnextTop
 Title   : _seqname
Usage : $obj->_seqname($seqname)
Function: internal
Example :
Returns : String
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);

  my ($seqname) = $self->_rearrange([qw(SEQNAME)], @args);

  # hardwire seq_id when creating gene and exon objects
$self->_seqname($seqname) if defined($seqname); return $self;
}
_initialize_statedescriptionprevnextTop
sub _initialize_state {
    my ($self,@args) = @_;

    # first call the inherited method!
$self->SUPER::_initialize_state(@args); # our private state variables
$self->{'_preds_parsed'} = 0; $self->{'_has_cds'} = 0; # array of pre-parsed predictions
$self->{'_preds'} = []; # seq stack
$self->{'_seqstack'} = [];
}
analysis_methoddescriptionprevnextTop
sub analysis_method {
#-------------
my ($self, $method) = @_; if($method && ($method !~ /Genemark\.hmm/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method);
}
next_featuredescriptionprevnextTop
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 $self->next_prediction(@args);
}
next_predictiondescriptionprevnextTop
sub next_prediction {
    my ($self) = @_;
    my $gene;

    # if the prediction section hasn't been parsed yet, we do this now
$self->_parse_predictions() unless $self->_predictions_parsed(); # get next gene structure
$gene = $self->_prediction(); return $gene;
}
_parse_predictionsdescriptionprevnextTop
sub _parse_predictions {
    my ($self) = @_;
    my %exontags = ('Initial' => 'Initial',
		    'Internal' => 'Internal',
		    'Terminal' => 'Terminal',
		    'Single' => '',
		    '_na_' => '');
    my $exontag;
    my $gene;
    my $exontype;
    my $current_gene_no = -1;

    # The prediction report does not contain a sequence identifier
# (at least the prokaryotic version doesn't)
my $seqname = $self->_seqname(); while(defined($_ = $self->_readline())) { if( (/^\s*(\d+)\s+(\d+)/) || (/^\s*(\d+)\s+[\+\-]/)) { # this is an exon, Genemark doesn't predict anything else
# $prednr corresponds to geneno.
my $prednr = $1; #exon no:
my $signalnr = 0; if ($2) { my $signalnr = $2; } # used in tag: exon_no
# split into fields
chomp(); my @flds = split(' ', $_); # create the feature (an exon) object
my $predobj = Bio::Tools::Prediction::Exon->new(); # define info depending on it being eu- or prokaryot
my ($start, $end, $orientation, $prediction_source); if ($self->analysis_method() =~ /PROKARYOTIC/i) { $prediction_source = "Genemark.hmm.pro"; $orientation = ($flds[1] eq '+') ? 1 : -1; ($start, $end) = @flds[(2,3)]; $exontag = "_na_"; } else { $prediction_source = "Genemark.hmm.eu"; $orientation = ($flds[2] eq '+') ? 1 : -1; ($start, $end) = @flds[(4,5)]; $exontag = $flds[3]; } # instatiate a location object via
# Bio::Factory::FTLocationFactory (to handle
# inexact coordinates)
my $location_string = join('..', $start, $end); my $location_factory = Bio::Factory::FTLocationFactory->new(); my $location_obj = $location_factory->from_string($location_string); $predobj->location($location_obj); #store the data in the exon object
$predobj->source_tag($prediction_source); $predobj->strand($orientation); $predobj->primary_tag($exontags{$exontag} . "Exon"); $predobj->add_tag_value('exon_no',"$signalnr") if ($signalnr); $predobj->is_coding(1); $predobj->seq_id($seqname) if (defined($seqname) && ($seqname ne 'unknown')); # frame calculation as in the genscan module
# is to be implemented...
#If the $prednr is not equal to the current gene, we
#need to make a new gene and close the old one
if($prednr != $current_gene_no) { # a new gene, store the old one if it exists
if (defined ($gene)) { $gene->seq_id($seqname); $gene = undef ; } #and make a new one
$gene = Bio::Tools::Prediction::Gene->new ( '-primary' => "GenePrediction$prednr", '-source' => $prediction_source); $self->_add_prediction($gene); $current_gene_no = $prednr; $gene->seq_id($seqname) if (defined($seqname) && ($seqname ne 'unknown')); } # Add the exon to the gene
$gene->add_exon($predobj, ($exontag eq "_na_" ? undef : $exontags{$exontag})); } if(/^(Genemark\.hmm\s*[PROKARYOTIC]*)\s+\(Version (.*)\)$/i) { $self->analysis_method($1); my $gm_version = $2; $self->analysis_method_version($gm_version); next; } #Matrix file for eukaryot version
if (/^Matrices file:\s+(\S+)?/i) { $self->analysis_subject($1); # since the line after the matrix file is always the date
# (in the output file's I have seen!) extract and store this
# here
if (defined(my $_date = $self->_readline())) { chomp ($_date); $self->analysis_date($_date); } } #Matrix file for prokaryot version
if (/^Model file name:\s+(\S+)/) { $self->analysis_subject($1); # since the line after the matrix file is always the date
# (in the output file's I have seen!) extract and store this
# here
my $_date = $self->_readline() ; if (defined($_date = $self->_readline())) { chomp ($_date); $self->analysis_date($_date); } } if(/^Sequence[ file]? name:\s+(.+)\s*$/i) { $seqname = $1; # $self->analysis_subject($seqname);
next; } /^>/ && do { $self->_pushback($_); # section of predicted aa sequences on recognition
# of a fasta start, read all sequences and find the
# appropriate gene
while (1) { my ($aa_id, $seq) = $self->_read_fasta_seq(); last unless ($aa_id); #now parse through the predictions to add the pred. protein
FINDPRED: foreach my $gene (@{$self->{'_preds'}}) { $gene->primary_tag() =~ /[^0-9]([0-9]+)$/; my $geneno = $1; if ($aa_id =~ /\|gene.$geneno\|/) { #print "x SEQ : \n $seq \nXXXX\n";
my $seqobj = Bio::Seq->new('-seq' => $seq, '-display_id' => $aa_id, '-alphabet' => "protein"); $gene->predicted_protein($seqobj); last FINDPRED; } } } last; }; } # if the analysis query object contains a ref to a Seq of PrimarySeq
# object, then extract the predicted sequences and add it to the gene
# object.
if (defined $self->analysis_query()) { my $orig_seq = $self->analysis_query(); FINDPREDSEQ: foreach my $gene (@{$self->{'_preds'}}) { my $predseq = ""; foreach my $exon ($gene->exons()) { #print $exon->start() . " " . $exon->end () . "\n";
$predseq .= $orig_seq->subseq($exon->start(), $exon->end()); } my $seqobj = Bio::PrimarySeq->new('-seq' => $predseq, '-display_id' => "transl"); $gene->predicted_cds($seqobj); } } $self->_predictions_parsed(1);
}
_predictiondescriptionprevnextTop
sub _prediction {
    my ($self) = @_;

    return unless(exists($self->{'_preds'}) && @{$self->{'_preds'}});
    return shift(@{$self->{'_preds'}});
}
_add_predictiondescriptionprevnextTop
sub _add_prediction {
    my ($self, $gene) = @_;

    if(! exists($self->{'_preds'})) {
	$self->{'_preds'} = [];
    }
    push(@{$self->{'_preds'}}, $gene);
}
_predictions_parseddescriptionprevnextTop
sub _predictions_parsed {
    my ($self, $val) = @_;

    $self->{'_preds_parsed'} = $val if $val;
    if(! exists($self->{'_preds_parsed'})) {
	$self->{'_preds_parsed'} = 0;
    }
    return $self->{'_preds_parsed'};
}
_has_cdsdescriptionprevnextTop
sub _has_cds {
    my ($self, $val) = @_;

    $self->{'_has_cds'} = $val if $val;
    if(! exists($self->{'_has_cds'})) {
	$self->{'_has_cds'} = 0;
    }
    return $self->{'_has_cds'};
}
_read_fasta_seqdescriptionprevnextTop
sub _read_fasta_seq {
    my ($self) = @_;
    my ($id, $seq);
    local $/ = ">";

    return 0 unless (my $entry = $self->_readline());

    $entry =~ s/^>//;
    # complete the entry if the first line came from a pushback buffer
while(! ($entry =~ />$/)) { last unless ($_ = $self->_readline()); $entry .= $_; } # delete everything onwards from an new fasta start (>)
$entry =~ s/\n>.*$//s; # id and sequence
if($entry =~ s/^(.+)\n//) { $id = $1; $id =~ s/ /_/g; $seq = $entry; $seq =~ s/\s//g; #print "\n@@ $id \n@@ $seq \n##\n";
} else { $self->throw("Can't parse Genemark predicted sequence entry"); } $seq =~ s/\s//g; # Remove whitespace
return ($id, $seq);
}
_seqnamedescriptionprevnextTop
sub _seqname {
    my ($self, $val) = @_;

    $self->{'_seqname'} = $val if $val;
    if(! exists($self->{'_seqname'})) {
        $self->{'_seqname'} = 'unknown';
    }
    return $self->{'_seqname'};
}

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 Lapp, Mark FiersTop
Email hlapp@gmx.net
m.w.e.j.fiers@plant.wag-ur.nl
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _