Bio::Tools Fgenesh
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Summary
Bio::Tools::Fgenesh - parse results of one Fgenesh run
Package variables
Privates (from "my" definitions)
%ExonTags = ('CDSf' => 'Initial', 'CDSi' => 'Internal', 'CDSl' => 'Terminal', 'CDSo' => 'Singleton')
Included modules
Bio::Root::Root
Bio::Tools::Prediction::Exon
Bio::Tools::Prediction::Gene
Symbol
Inherit
Bio::Tools::AnalysisResult
Synopsis
   use Bio::Tools::Fgenesh;
$fgenesh = Bio::Tools::Fgenesh->new(-file => 'result.fgenesh'); # filehandle: $fgenesh = Bio::Tools::Fgenesh->new( -fh => \*INPUT ); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $fgensh->next_feature() is the same while($gene = $fgenesh->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) $fgenesh->close();
Description
The Fgenesh module provides a parser for Fgenesh (version 2) gene structure
prediction output. It parses one gene prediction into a
Bio::SeqFeature::Gene::Transcript- derived object.
This module also implements the Bio::SeqAnalysisParserI interface, and thus
can be used wherever such an object fits.
Methods
_initialize_state
No description
Code
analysis_methodDescriptionCode
next_featureDescriptionCode
next_predictionDescriptionCode
_parse_predictionsDescriptionCode
_predictionDescriptionCode
_add_predictionDescriptionCode
_predictions_parsedDescriptionCode
_has_cdsDescriptionCode
_read_fasta_seqDescriptionCode
Methods description
analysis_methodcode    nextTop
 Usage     : $genscan->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/genscan/i.
Returns : String
Argument : n/a
next_featurecodeprevnextTop
 Title   : next_feature
Usage : while($gene = $fgenesh->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the Fgenesh result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Example : Returns : A Bio::Tools::Prediction::Gene object. Args :
next_predictioncodeprevnextTop
 Title   : next_prediction
Usage : while($gene = $fgenesh->next_prediction()) { ... }
Function: Returns the next gene structure prediction of the Genscan 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
$self->_readline() to retrieve input, and is able to strip off
the traling description lines.
Example :
Returns : An array of two elements: fasta_id & sequence
Methods code
_initialize_statedescriptionprevnextTop
sub _initialize_state {
    my ($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 !~ /fgenesh/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 = $self->_prediction(); if($gene) { # fill in predicted protein, and if available the predicted CDS
#
# use the seq stack if there's a seq on it
my $seqobj = pop(@{$self->{'_seqstack'}}); my ($id, $seq); unless ($seqobj) { ($id, $seq) = $self->_read_fasta_seq(); my $alphabet; if (($id =~ /mrna/) || ($id =~ /cds/)) { $alphabet = 'dna'; } else { $alphabet = 'protein'; } $seqobj = Bio::PrimarySeq->new('-seq' => $seq, '-display_id' => $id, '-alphabet' => $alphabet); } if ($seqobj) { # check that prediction number matches the prediction number
# indicated in the sequence id (there may be incomplete gene
# predictions that contain only signals with no associated protein
# prediction.
$gene->primary_tag() =~ /[^0-9]([0-9]+)$/; my $prednr = $1; if ($id !~ /_predicted_(\w+)_$prednr/) { # this is not our sequence, so push back for next prediction
push(@{$self->{'_seqstack'}}, $seqobj); } else { if ($1 eq "protein") { $gene->predicted_protein($seqobj); } elsif (($1 eq "mrna") || ($1 eq "cds")) { $self->_has_cds(1); $gene->predicted_cds($seqobj); # Have to go back in and get the protein...
($id, $seq) = $self->_read_fasta_seq(); if ($id =~ /_cds_/) { ($id, $seq) = $self->_read_fasta_seq(); } $seqobj = Bio::PrimarySeq->new('-seq' => $seq, '-display_id' => $id, '-alphabet' => "protein"); $gene->predicted_protein($seqobj); } } } } return $gene;
}
_parse_predictionsdescriptionprevnextTop
sub _parse_predictions {
    my ($self) = @_;
    my $gene;
    my $seqname;

    while(defined($_ = $self->_readline())) {

	if(/^\s*(\d+)\s+([+\-])/) {
            my $line = $_;

	    # exon or signal
my $prednr = $1; my $strand = ($2 eq '+') ? 1 : -1; if(! defined($gene)) { $gene = Bio::Tools::Prediction::Gene->new( '-primary' => "GenePrediction$prednr", '-source' => 'Fgenesh'); } # split into fields
chomp(); my @flds = split(/\s+/, ' ' . $line); ## NB - the above adds leading whitespace before the gene
## number in case there was none (as quick patch to code
## below which expects it but it is not present after 999
## predictions!) This allows >999 predictions to be parsed.
# create the feature object depending on the type of signal
my $predobj; my $is_exon = grep {$line =~ $_} keys(%ExonTags); my ($start, $end); if($is_exon) { $predobj = Bio::Tools::Prediction::Exon->new(); $predobj->score($flds[8]); $start = $flds[5]; $end = $flds[7]; } else { # PolyA site, or TSS
$predobj = Bio::SeqFeature::Generic->new(); $predobj->score($flds[5]); $start = $flds[4]; $end = $flds[4]; } # set common fields
$predobj->source_tag('Fgenesh'); $predobj->strand($strand); # Following tactical commenting-out made by
# malcolm.cook@stowers-institute.org since coordinate reversal is
# apparently vestigial copy/paste detritus from Genscan.pm origins of
# this module and this is NOT needed for fgenesh (at least in v
# 2.1.4).
# if($predobj->strand() == 1) {
$predobj->start($start); $predobj->end($end); # } else {
# $predobj->end($start);
# $predobj->start($end);
# }
# print STDERR "start $start end $end\n";
# add to gene structure (should be done only when start and end
# are set, in order to allow for proper expansion of the range)
if($is_exon) { # first, set fields unique to exons
$predobj->primary_tag($ExonTags{$flds[4]} . 'Exon'); $predobj->is_coding(1); my $cod_offset; if($predobj->strand() == 1) { $cod_offset = ($flds[9] - $predobj->start()) % 3; # Possible values are -2, -1, 0, 1, 2. -1 and -2 correspond
# to offsets 2 and 1, resp. Offset 3 is the same as 0.
$cod_offset += 3 if($cod_offset < 1); } else { # On the reverse strand the Genscan frame also refers to
# the first base of the first complete codon, but viewed
# from forward, which is the third base viewed from
# reverse.
$cod_offset = ($flds[11] - $predobj->end()) % 3; # Possible values are -2, -1, 0, 1, 2. Due to the reverse
# situation, {2,-1} and {1,-2} correspond to offsets
# 1 and 2, resp. Offset 3 is the same as 0.
$cod_offset -= 3 if($cod_offset >= 0); $cod_offset = -$cod_offset; } # Offsets 2 and 1 correspond to frame 1 and 2 (frame of exon
# is the frame of the first base relative to the exon, or the
# number of bases the first codon is missing).
$predobj->frame(3 - $cod_offset); # print STDERR " frame is " . $predobj->frame() . "\n";
# then add to gene structure object
$gene->add_exon($predobj, $ExonTags{$flds[1]}); } elsif($flds[3] eq 'PolA') { $predobj->primary_tag("PolyAsite"); $gene->poly_A_site($predobj); } elsif($flds[3] eq 'TSS') { $predobj->primary_tag("Promoter"); # (hey! a TSS is NOT a promoter... what's going on here?...
$gene->add_promoter($predobj); #I'd like to do this (for now):
#$predobj->primary_tag("TSS"); #this is not the right model, but, it IS a feature at least.
#but the followg errs out
#$gene->add_SeqFeature($predobj); #err: MSG: start is undefined when bounds at Bio::SeqFeature::Generic::add_SeqFeature 671 check since gene has no start yet
} else { $self->throw("unrecognized prediction line: " . $line); } next; } if(/^\s*$/ && defined($gene)) { # current gene is completed
$gene->seq_id($seqname); $self->_add_prediction($gene); $gene = undef; next; } if(/^(FGENESH)\s+([\d\.]+)/) { $self->analysis_method($1); $self->analysis_method_version($2); if (/\s(\S+)\sgenomic DNA/) { $self->analysis_subject($1); } next; } if(/^\s*Seq name:\s+(\S+)/) { $seqname = $1; next; } /^Predicted protein/ && do { # section of predicted sequences
$self->_pushback($_); last; }; } $self->_predictions_parsed(1);
}
_predictiondescriptionprevnextTop
sub _prediction {
    my ($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 $/ = ">";
my $entry = $self->_readline(); # print " ^^ $entry\n";
return unless ($entry); $entry = $self->_readline() if ($entry =~ /^Predicted protein/); # print " ^^ $entry\n";
# Pick up the header / id.
if ($entry =~ /^>FGENESH:/) { if ($entry =~ /^>FGENESH:\s+(\d+)/) { # print STDERR " this is a predicted gene\n";
$id = "_predicted_protein_" . $1; } elsif ($entry =~ /^>FGENESH:\[mRNA\]\s*(\d+)/) { # print STDERR " this is an mRNA\n";
$id = "_predicted_mrna_" . $1; } elsif ($entry =~ /^>FGENESH:\[exon\]\s+Gene:\s*(\d+)/) { $id = "_predicted_cds_" . $1; } $seq = ""; $entry = $self->_readline(); } my $done = 0; while (!$done) { # print "*** $entry\n";
if (($entry =~ /^>FGENESH:\[exon\]/) && ($id =~ /^_predicted_cds_/)) { # print STDERR " -- informed about an exon header...\n";
$entry = $self->_readline(); } else { $seq .= $entry; # print STDERR " Added $entry\n";
} last unless $entry = $self->_readline(); if (($entry =~ /^>/) && (!(($entry =~ /^>FGENESH:\[exon\]/) && ($id =~ /^_predicted_cds_/)))) { $self->_pushback($entry); last; } } # id and sequence
$seq =~ s/\s//g; # Remove whitespace
return ($id, $seq); } 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 - Chris DwanTop
Email chris-at-dwan.org
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _