Raw content of Bio::Tools::MZEF
<![CDATA[# $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;
]]>