#
# BioPerl module for Bio::Tools::Glimmer
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl-dot-org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and
GlimmerM/GlimmerHMM eukaryotic gene predictions
=head1 SYNOPSIS
use Bio::Tools::Glimmer;
# file
my $parser = Bio::Tools::Glimmer->new(-file => $file);
# filehandle:
$parser = Bio::Tools::Glimmer->new( -fh => \*INPUT );
# provide a sequence identifier (Glimmer 2.X)
my $parser = Bio::Tools::Glimmer->new(-file => $file, -seqname => seqname);
# force format (override automatic detection)
my $parser = Bio::Tools::Glimmer->new(-file => $file, -format => 'GlimmerM');
# parse the results
# note: this class is-a Bio::Tools::AnalysisResult which implements
# Bio::SeqAnalysisParserI, i.e., $glimmer->next_feature() is the same
while(my $gene = $parser->next_prediction()) {
# For eukaryotic input (GlimmerM/GlimmerHMM), $gene will be an instance
# of Bio::Tools::Prediction::Gene, which inherits off
# Bio::SeqFeature::Gene::Transcript, and $gene->exons() will return an
# array of Bio::Tools::Prediction::Exon objects.
# For prokaryotic input (Glimmer2.X/Glimmer3.X), $gene will be an
# instance of Bio::SeqFeature::Generic
# all exons (eukaryotic only):
@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');
}
=head1 DESCRIPTION
This is a module for parsing Glimmer, GlimmerM and GlimmerHMM predictions.
It will create gene objects from the prediction report which can
be attached to a sequence using Bioperl objects, or output as GFF
suitable for loading into Bio::DB::GFF for use with Gbrowse.
Glimmer is open source and available at
L<http://www.cbcb.umd.edu/software/glimmer/>.
GlimmerM is open source and available at
L<http://www.tigr.org/software/glimmerm/>.
GlimmerHMM is open source and available at
L<http://www.cbcb.umd.edu/software/GlimmerHMM/>.
Note that Glimmer 2.X will only process the first
sequence in a fasta file, and the prediction report does not contain any
sort of sequence identifier
Note that Glimmer 3.X produces two output files. This module only parses
the .predict file.
=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
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
=head1 CONTRIBUTORS
Torsten Seemann
Mark Johnson
=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::Glimmer;
use strict;
use Bio::Factory::FTLocationFactory;
use Bio::Tools::Prediction::Gene;
use Bio::Tools::Prediction::Exon;
use base qw(Bio::Tools::AnalysisResult);
sub _initialize_state {
my($self,@args) = @_;
# first call the inherited method!
my $make = $self->SUPER::_initialize_state(@args);
$self->{'_preds_parsed'} = 0;
# array of pre-parsed predictions
$self->{'_preds'} = [];
}
=head2 new
Title : new
Usage : my $obj = Bio::Tools::Glimmer->new();
Function: Builds a new Bio::Tools::Glimmer object
Returns : an instance of Bio::Tools::Glimmer
Args : format ('Glimmer', 'GlimmerM', 'GlimmerHMM'), seqname
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($format, $seqname, $seqlength, $detail) =
$self->_rearrange([qw(FORMAT SEQNAME SEQLENGTH DETAIL)], @args);
# override automagic format detection
if (defined($format) &&
(($format eq 'Glimmer') ||
($format eq 'GlimmerM') ||
($format eq 'GlimmerHMM'))
) {
$self->_format($format);
}
if (defined($detail)) {
$self->_format('Glimmer');
$self->_detail_file($detail);
}
# hardwire seq_id when creating gene and exon objects (Glimmer 2.X)
$self->_seqname($seqname) if defined($seqname);
# store the length of the input sequence (Glimmer 2.X)
$self->_seqlength($seqlength) if defined($seqlength);
return $self;
}
=head2 analysis_method
Usage : $glimmer->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/glimmer/i.
Returns : String
Argument : n/a
=cut
#-------------
sub analysis_method {
#-------------
my ($self, $method) = @_;
if($method && ($method !~ /glimmer/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 = $glimmer->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the Glimmer result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
=cut
sub next_feature {
my ($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 = $glimmer->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the Glimmer result
file. Call this method repeatedly until FALSE is returned.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
=cut
sub next_prediction {
my ($self) = @_;
my $gene;
# if the prediction section hasn't been parsed yet, we do this now
$self->_parse_predictions() unless $self->_predictions_parsed();
# get next gene structure
$gene = $self->_prediction();
return $gene;
}
=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 = (
'Glimmer' => '_parse_prokaryotic',
'GlimmerM' => '_parse_eukaryotic',
'GlimmerHMM' => '_parse_eukaryotic',
'_DEFAULT_' => '_parse_eukaryotic',
);
my $format = $self->_format();
if (!$format) {
while (my $line = $self->_readline()) {
if ( $line =~ /^Glimmer\S*\s+\(Version\s*\S+\)/ ) {
$format = 'GlimmerM';
$self->_pushback($line);
last;
}
elsif ( $line =~ /^Glimmer\S*$/ ) {
$format = 'GlimmerHMM';
$self->_pushback($line);
last;
}
elsif ($line =~ /^Putative Genes:$/) {
$format = 'Glimmer';
$self->_pushback($line);
last;
}
elsif ($line =~ /^>(\S+)/) {
$format = 'Glimmer';
$self->_pushback($line);
last;
}
}
}
my $method =
(exists($method{$format})) ? $method{$format} : $method{'_DEFAULT_'};
return $self->$method();
}
=head2 _parse_eukaryotic
Title : _parse_eukaryotic()
Usage : $obj->_parse_eukaryotic()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
=cut
sub _parse_eukaryotic {
my ($self) = @_;
my ($gene,$seqname,$seqlen,$source,$lastgenenum);
while(defined($_ = $self->_readline())) {
if( /^(Glimmer\S*)\s+\(Version\s*(\S+)\)/ ) {
$source = "$1_$2";
next;
} elsif( /^(GlimmerHMM\S*)$/ ) { # GlimmerHMM has no version
$source = $1;
next;
} elsif(/^Sequence name:\s+(.+)$/ ) {
$seqname = $1;
next;
} elsif( /^Sequence length:\s+(\S+)/ ) {
$seqlen = $1;
next;
} elsif( m/^(Predicted genes)|(Gene)|\s+\#/ || /^\s+$/ ) {
next;
} elsif( # GlimmerM/HMM gene-exon prediction line
/^\s+(\d+)\s+ # gene num
(\d+)\s+ # exon num
([\+\-])\s+ # strand
(\S+)\s+ # exon type
(\d+)\s+(\d+) # exon start, end
\s+(\d+) # exon length
/ox ) {
my ($genenum,$exonnum,$strand,$type,$start,$end,$len) =
( $1,$2,$3,$4,$5,$6,$7);
if( ! $lastgenenum || $lastgenenum != $genenum) {
$self->_add_prediction($gene) if ( $gene );
$gene = Bio::Tools::Prediction::Gene->new
(
'-seq_id' => $seqname,
'-primary_tag' => "gene",
'-source_tag' => $source,
'-tag' => { 'Group' => "GenePrediction$genenum"},
);
}
my $exon = Bio::Tools::Prediction::Exon->new
('-seq_id' => $seqname,
'-start' => $start,
'-end' => $end,
'-strand' => $strand eq '-' ? '-1' : '1',
'-source_tag' => $source,
'-primary_tag'=> 'exon',
'-tag' => { 'Group' => "GenePrediction$genenum"},
);
$gene->add_exon($exon,lc($type));
$lastgenenum = $genenum;
}
}
$self->_add_prediction($gene) if( $gene );
$self->_predictions_parsed(1);
}
=head2 _parse_prokaryotic
Title : _parse_prokaryotic()
Usage : $obj->_parse_prokaryotic()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
=cut
sub _parse_prokaryotic {
my ($self) = @_;
# default value, possibly overriden later
my $source = 'Glimmer';
# Store the sequence length(s) here, either from the
# seqlength arg to the constructor, or from the
# Glimmer 3.X detail file
my %seqlength = ( );
# Glimmer 2.X does not provide a sequence identifer
# in the prediction report (will default to unknown
# if not specified in the seqname arg to the
# constructor
#
# Glimmer 2.X does not report the length of the
# input sequence, either (will default to undef
# if not specified in the seqlength arg to the
# constructor
my $seqname = $self->_seqname();
my $seqlength = $self->_seqlength();
if (defined($seqlength)) {
$seqlength{$seqname} = $seqlength
}
# Parse the detail file, if we have one (Glimmer 3.X)
my $detail_file = $self->_detail_file();
if (defined($detail_file)) {
my $io = Bio::Root::IO->new(-file => $detail_file);
my $seqname;
while (defined($_ = $io->_readline())) {
if ($_ =~ /^>(\S+)/) {
$seqname = $1;
next;
}
if (defined($seqname) && ($_ =~ /^Sequence length = (\d+)$/)) {
$seqlength{$seqname} = $1;
next;
}
}
}
my $location_factory = Bio::Factory::FTLocationFactory->new();
while(defined($_ = $self->_readline())) {
# Glimmer 3.X does provide a sequence identifier -
# beware whitespace at the end (comes through from
# the fasta file)
if ($_ =~ /^Putative Genes:$/) {
$source = 'Glimmer_2.X';
next;
}
# Glimmer 3.X sequence identifier
elsif ($_ =~ /^>(\S+)/) {
$seqname = $1;
$seqlength = $seqlength{$seqname};
$source = 'Glimmer_3.X';
next;
}
elsif (
# Glimmer 2.X prediction
(/^\s+(\d+)\s+ # gene num
(\d+)\s+(\d+)\s+ # start, end
\[([\+\-])(\d{1})\s+ # strand, frame
/ox ) ||
# Glimmer 3.X prediction
(/^[^\d]+(\d+)\s+ # orf (numeric portion)
(\d+)\s+(\d+)\s+ # start, end
([\+\-])(\d{1})\s+ # strand, frame
([\d\.]+) # score
/ox)) {
my ($genenum,$start,$end,$strand,$frame,$score) =
( $1,$2,$3,$4,$5,$6 );
my $circular_prediction = 0;
# Check for a circular prediction before we
# start fiddling with the coordinates
if ($strand eq '+') {
if ($start > $end) {
$circular_prediction = 1;
}
}
else {
if ($start < $end) {
$circular_prediction = 1;
}
}
if ($circular_prediction) {
unless (defined($seqlength)) {
$self->throw("need to know the sequence length to handle wraparound genes");
}
}
# Glimmer 2.X predictions do not include
# the stop codon - this might extend the
# prediction off either end of the sequence.
# This works fine even on circular/wraparound
# predictions.
if ($source eq 'Glimmer_2.X') {
if ($strand eq '+') {
$end += 3;
}
else {
$end -= 3;
}
}
# We might have extended a Glimmer 2.X prediction
# beyond the boundaries of the input sequence.
# Also, Glimmer 3.X (with -X) will output predictions
# with coordinates less than 1 or greater than the
# length of the sequence.
my ($fst, $fend);
foreach my $coord ($start, $end) {
if ($coord < 1) {
$coord = '<1';
$fst++;
} elsif (defined($seqlength) && ($coord > $seqlength)) {
$coord = ">$seqlength";
$fend++;
}
}
my $location_string;
if ($circular_prediction) {
if ($strand eq '+') {
$location_string = "join($start..$seqlength,1..$end)";
}
else {
$location_string = "join($start..1,$seqlength..$end)";
}
}
else {
# start must always be less than end for gene locations
if ($strand eq '-' && !$fst && !$fend && $start > $end) {
($start, $end) = ($end, $start);
}
$location_string = "$start..$end";
}
my $location_object =
$location_factory->from_string($location_string);
# convert glimmer's frame range from 1-3 to SeqFeature's 0-2.
$frame--;
my $gene = Bio::SeqFeature::Generic->new
(
'-seq_id' => $seqname,
'-location' => $location_object,
'-strand' => $strand eq '-' ? '-1' : '1',
'-frame' => $frame,
'-source_tag' => $source,
'-display_name' => "orf$genenum",
'-primary_tag'=> 'gene',
'-tag' => { 'Group' => "GenePrediction_$genenum"},
'-score' => $score || undef
);
$self->_add_prediction($gene)
}
}
$self->_predictions_parsed(1);
}
=head2 _prediction
Title : _prediction()
Usage : $gene = $obj->_prediction()
Function: internal
Example :
Returns :
=cut
sub _prediction {
my ($self) = @_;
return 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'};
}
=head2 _seqname
Title : _seqname
Usage : $obj->_seqname($seqname)
Function: internal (for Glimmer 2.X)
Example :
Returns : String
=cut
sub _seqname {
my ($self, $val) = @_;
$self->{'_seqname'} = $val if $val;
if(! exists($self->{'_seqname'})) {
$self->{'_seqname'} = 'unknown';
}
return $self->{'_seqname'};
}
=head2 _seqlength
Title : _seqlength
Usage : $obj->_seqlength($seqlength)
Function: internal (for Glimmer 2.X)
Example :
Returns : String
=cut
sub _seqlength {
my ($self, $val) = @_;
$self->{'_seqlength'} = $val if $val;
return $self->{'_seqlength'};
}
=head2 _format
Title : _format
Usage : $obj->_format($format)
Function: internal
Example :
Returns : String
=cut
sub _format {
my ($self, $val) = @_;
$self->{'_format'} = $val if $val;
return $self->{'_format'};
}
=head2 _detail_file
Title : _detail_file
Usage : $obj->_detail_file($filename)
Function: internal (for Glimmer 3.X)
Example :
Returns : String
=cut
sub _detail_file {
my ($self, $val) = @_;
$self->{'_detail_file'} = $val if $val;
return $self->{'_detail_file'};
}
1;