#
# BioPerl module for Bio::SearchIO::exonerate
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl.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::SearchIO::exonerate - parser for Exonerate
=head1 SYNOPSIS
# do not use this module directly, it is a driver for SearchIO
use Bio::SearchIO;
my $searchio = Bio::SearchIO->new(-file => 'file.exonerate',
-format => 'exonerate');
while( my $r = $searchio->next_result ) {
print $r->query_name, "\n";
}
=head1 DESCRIPTION
This is a driver for the SearchIO system for parsing Exonerate (Guy
Slater) output. You can get Exonerate at
http://www.ebi.ac.uk/~guy/exonerate/
[until Guy puts up a Web reference,publication for it.]).
An optional parameter -min_intron is supported by the L<new>
initialization method. This is if you run Exonerate with a different
minimum intron length (default is 30) the parser will be able to
detect the difference between standard deletions and an intron. Still
some room to play with there that might cause this to get
misinterpreted that has not been fully tested or explored.
The VULGAR and CIGAR formats should be parsed okay now creating HSPs
where appropriate (so merging match states where appropriate rather
than breaking an HSP at each indel as it may have done in the past).
The GFF that comes from exonerate is still probably a better way to go
if you are doing protein2genome or est2genome mapping.
For example you can see this script:
### TODO: Jason, this link is dead, do we have an updated one?
http://fungal.genome.duke.edu/~jes12/software/scripts/process_exonerate_gff3.perl.txt
If your report contains both CIGAR and VULGAR lines only the first one
will processed for a given Query/Target pair. If you preferentially
want to use VULGAR or CIGAR add one of these options when initializing
the SearchIO object.
-cigar => 1
OR
-vulgar => 1
Or set them via these methods.
$parser->cigar(1)
OR
$parser->vulgar(1)
=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 the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=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::SearchIO::exonerate;
use strict;
use vars qw(@STATES %MAPPING %MODEMAP $DEFAULT_WRITER_CLASS $MIN_INTRON);
use base qw(Bio::SearchIO);
%MODEMAP = ( 'ExonerateOutput' => 'result',
'Hit' => 'hit',
'Hsp' => 'hsp'
);
%MAPPING =
(
'Hsp_query-from'=> 'HSP-query_start',
'Hsp_query-to' => 'HSP-query_end',
'Hsp_hit-from' => 'HSP-hit_start',
'Hsp_hit-to' => 'HSP-hit_end',
'Hsp_qseq' => 'HSP-query_seq',
'Hsp_hseq' => 'HSP-hit_seq',
'Hsp_midline' => 'HSP-homology_seq',
'Hsp_score' => 'HSP-score',
'Hsp_qlength' => 'HSP-query_length',
'Hsp_hlength' => 'HSP-hit_length',
'Hsp_align-len' => 'HSP-hsp_length',
'Hsp_identity' => 'HSP-identical',
'Hsp_gaps' => 'HSP-hsp_gaps',
'Hsp_hitgaps' => 'HSP-hit_gaps',
'Hsp_querygaps' => 'HSP-query_gaps',
'Hit_id' => 'HIT-name',
'Hit_desc' => 'HIT-description',
'Hit_len' => 'HIT-length',
'Hit_score' => 'HIT-score',
'ExonerateOutput_program' => 'RESULT-algorithm_name',
'ExonerateOutput_query-def' => 'RESULT-query_name',
'ExonerateOutput_query-desc'=> 'RESULT-query_description',
'ExonerateOutput_query-len' => 'RESULT-query_length',
);
$DEFAULT_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter';
$MIN_INTRON=30; # This is the minimum intron size
=head2 new
Title : new
Usage : my $obj = Bio::SearchIO::exonerate->new();
Function: Builds a new Bio::SearchIO::exonerate object
Returns : an instance of Bio::SearchIO::exonerate
Args : -min_intron => somewhat obselete option, how to determine if a
an indel is an intron or a local gap. Use VULGAR
rather than CIGAR to avoid this heuristic,default 30.
-cigar => 1 set this to 1 if you want to parse
CIGAR exclusively.
-vulgar => 1 set this to 1 if you want to parse VULGAR
exclusively, setting both to 1 will revert
to the default behavior of just parsing the
first line that it sees.
=cut
sub new {
my ($class) = shift;
my $self = $class->SUPER::new(@_);
my ($min_intron,$cigar,
$vulgar) = $self->_rearrange([qw(MIN_INTRON
CIGAR
VULGAR)], @_);
if( $min_intron ) {
$MIN_INTRON = $min_intron;
}
if( $cigar && $vulgar ) {
$self->warn("cannot get HSPs from both CIGAR and VULGAR lines, will just choose whichever comes first (same as if you had chosen neither");
$cigar = 0; $vulgar=0;
}
$self->cigar($cigar);
$self->vulgar($vulgar);
$self;
}
=head2 next_result
Title : next_result
Usage : my $hit = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
Args : none
=cut
sub next_result{
my ($self) = @_;
local $/ = "\n";
local $_;
$self->{'_last_data'} = '';
my ($reporttype,$seenquery,$reportline);
$self->start_document();
my @hit_signifs;
my $seentop;
my (@q_ex, @m_ex, @h_ex); ## gc addition
while( defined($_ = $self->_readline) ) {
# warn( "Reading $_");
if( /^\s*Query:\s+(\S+)\s*(.+)?/ ) {
if( $seentop ) {
$self->end_element({'Name' => 'ExonerateOutput'});
$self->_pushback($_);
return $self->end_document();
}
$seentop = 1;
my ($nm,$desc) = ($1,$2);
chomp($desc) if defined $desc;
$self->{'_result_count'}++;
$self->start_element({'Name' => 'ExonerateOutput'});
$self->element({'Name' => 'ExonerateOutput_query-def',
'Data' => $nm });
$self->element({'Name' => 'ExonerateOutput_query-desc',
'Data' => $desc });
$self->element({'Name' => 'ExonerateOutput_program',
'Data' => 'Exonerate' });
$self->{'_seencigar'} = 0;
$self->{'_vulgar'} = 0;
} elsif ( /^Target:\s+(\S+)\s*(.+)?/ ) {
my ($nm,$desc) = ($1,$2);
chomp($desc) if defined $desc;
$self->start_element({'Name' => 'Hit'});
$self->element({'Name' => 'Hit_id',
'Data' => $nm});
$self->element({'Name' => 'Hit_desc',
'Data' => $desc});
$self->{'_seencigar'} = 0;
$self->{'_vulgar'} = 0;
} elsif( s/^vulgar:\s+(\S+)\s+ # query sequence id
(\d+)\s+(\d+)\s+([\-\+\.])\s+ # query start-end-strand
(\S+)\s+ # target sequence id
(\d+)\s+(\d+)\s+([\-\+])\s+ # target start-end-strand
(-?\d+)\s+ # score
//ox ) {
next if( $self->cigar || $self->{'_seencigar'});
$self->{'_vulgar'}++;
#
# Note from Ewan. This is ugly - copy and paste from
# cigar line parsing. Should unify somehow...
#
if( ! $self->within_element('result') ) {
$self->start_element({'Name' => 'ExonerateOutput'});
$self->element({'Name' => 'ExonerateOutput_query-def',
'Data' => $1 });
}
if( ! $self->within_element('hit') ) {
$self->start_element({'Name' => 'Hit'});
$self->element({'Name' => 'Hit_id',
'Data' => $5});
}
## gc note:
## $qe and $he are no longer used for calculating the ends,
## just the $qs and $hs values and the alignment and insert lenghts
my ($qs,$qe,$qstrand) = ($2,$3,$4);
my ($hs,$he,$hstrand) = ($6,$7,$8);
my $score = $9;
# $self->element({'Name' => 'ExonerateOutput_query-len',
# 'Data' => $qe});
# $self->element({'Name' => 'Hit_len',
# 'Data' => $he});
## gc note:
## add one because these values are zero-based
## this calculation was originally done lower in the code,
## but it's clearer to do it just once at the start
my @rest = split;
my ($qbegin,$qend) = ('query-from', 'query-to');
if( $qstrand eq '-' ) {
$qstrand = -1; $qe++;
} else {
$qstrand = 1;
$qs++;
}
my ($hbegin,$hend) = ('hit-from', 'hit-to');
if( $hstrand eq '-' ) {
$hstrand = -1;
$he++;
} else {
$hstrand = 1;
$hs++;
}
# okay let's do this right and generate a set of HSPs
# from the cigar line/home/bio1/jes12/bin/exonerate --model est2genome --bestn 1 t/data/exonerate_cdna.fa t/data/exonerate_genomic_rev.fa
my ($aln_len,$inserts,$deletes) = (0,0,0);
my ($laststate,@events,$gaps) =( '' );
while( @rest >= 3 ) {
my ($state,$len1,$len2) = (shift @rest, shift @rest, shift @rest);
#
# HSPs are only the Match cases; otherwise we just
# move the coordinates on by the correct amount
#
if( $state eq 'M' ) {
if( $laststate eq 'G' ) {
# merge gaps across Match states so the HSP
# goes across
$events[-1]->{$qend} = $qs + $len1*$qstrand - $qstrand;
$events[-1]->{$hend} = $hs + $len2*$hstrand - $hstrand;
$events[-1]->{'gaps'} = $gaps;
} else {
push @events,
{ 'score' => $score,
'align-len' => $len1,
$qbegin => $qs,
$qend => ($qs + $len1*$qstrand - $qstrand),
$hbegin => $hs,
$hend => ($hs + $len2*$hstrand - $hstrand),
};
}
$gaps = 0;
} else {
$gaps = $len1 + $len2 if $state eq 'G';
}
$qs += $len1*$qstrand;
$hs += $len2*$hstrand;
$laststate= $state;
}
for my $event ( @events ) {
$self->start_element({'Name' => 'Hsp'});
while( my ($key,$val) = each %$event ) {
$self->element({'Name' => "Hsp_$key",
'Data' => $val});
}
$self->element({'Name' => 'Hsp_identity',
'Data' => 0});
$self->end_element({'Name' => 'Hsp'});
}
# end of hit
$self->element({'Name' => 'Hit_score',
'Data' => $score});
# issued end...
$self->end_element({'Name' => 'Hit'});
$self->end_element({'Name' => 'ExonerateOutput'});
return $self->end_document();
} elsif( s/^cigar:\s+(\S+)\s+ # query sequence id
(\d+)\s+(\d+)\s+([\-\+])\s+ # query start-end-strand
(\S+)\s+ # target sequence id
(\d+)\s+(\d+)\s+([\-\+])\s+ # target start-end-strand
(-?\d+)\s+ # score
//ox ) {
next if( $self->vulgar || $self->{'_seenvulgar'});
$self->{'_cigar'}++;
if( ! $self->within_element('result') ) {
$self->start_element({'Name' => 'ExonerateOutput'});
$self->element({'Name' => 'ExonerateOutput_query-def',
'Data' => $1 });
}
if( ! $self->within_element('hit') ) {
$self->start_element({'Name' => 'Hit'});
$self->element({'Name' => 'Hit_id',
'Data' => $5});
}
## gc note:
## $qe and $he are no longer used for calculating the ends,
## just the $qs and $hs values and the alignment and insert lenghts
my ($qs,$qe,$qstrand) = ($2,$3,$4);
my ($hs,$he,$hstrand) = ($6,$7,$8);
my $score = $9;
# $self->element({'Name' => 'ExonerateOutput_query-len',
# 'Data' => $qe});
# $self->element({'Name' => 'Hit_len',
# 'Data' => $he});
my @rest = split;
if( $qstrand eq '-' ) {
$qstrand = -1;
($qs,$qe) = ($qe,$qs); # flip-flop if we're on opp strand
$qs--; $qe++;
} else { $qstrand = 1; }
if( $hstrand eq '-' ) {
$hstrand = -1;
($hs,$he) = ($he,$hs); # flip-flop if we're on opp strand
$hs--; $he++;
} else { $hstrand = 1; }
# okay let's do this right and generate a set of HSPs
# from the cigar line
## gc note:
## add one because these values are zero-based
## this calculation was originally done lower in the code,
## but it's clearer to do it just once at the start
$qs++; $hs++;
my ($aln_len,$inserts,$deletes) = (0,0,0);
while( @rest >= 2 ) {
my ($state,$len) = (shift @rest, shift @rest);
if( $state eq 'I' ) {
$inserts+=$len;
} elsif( $state eq 'D' ) {
if( $len >= $MIN_INTRON ) {
$self->start_element({'Name' => 'Hsp'});
$self->element({'Name' => 'Hsp_score',
'Data' => $score});
$self->element({'Name' => 'Hsp_align-len',
'Data' => $aln_len});
$self->element({'Name' => 'Hsp_identity',
'Data' => $aln_len -
($inserts + $deletes)});
# HSP ends where the other begins
$self->element({'Name' => 'Hsp_query-from',
'Data' => $qs});
## gc note:
## $qs is now the start of the next hsp
## the end of this hsp is 1 before this position
## (or 1 after in case of reverse strand)
$qs += $aln_len*$qstrand;
$self->element({'Name' => 'Hsp_query-to',
'Data' => $qs - ($qstrand*1)});
$hs += $deletes*$hstrand;
$self->element({'Name' => 'Hsp_hit-from',
'Data' => $hs});
$hs += $aln_len*$hstrand;
$self->element({'Name' => 'Hsp_hit-to',
'Data' => $hs-($hstrand*1)});
$self->element({'Name' => 'Hsp_align-len',
'Data' => $aln_len + $inserts
+ $deletes});
$self->element({'Name' => 'Hsp_identity',
'Data' => $aln_len });
$self->element({'Name' => 'Hsp_gaps',
'Data' => $inserts + $deletes});
$self->element({'Name' => 'Hsp_querygaps',
'Data' => $inserts});
$self->element({'Name' => 'Hsp_hitgaps',
'Data' => $deletes});
## gc addition start
$self->element({'Name' => 'Hsp_qseq',
'Data' => shift @q_ex,
});
$self->element({'Name' => 'Hsp_hseq',
'Data' => shift @h_ex,
});
$self->element({'Name' => 'Hsp_midline',
'Data' => shift @m_ex,
});
## gc addition end
$self->end_element({'Name' => 'Hsp'});
$aln_len = $inserts = $deletes = 0;
}
$deletes+=$len;
} else {
$aln_len += $len;
}
}
$self->start_element({'Name' => 'Hsp'});
## gc addition start
$self->element({'Name' => 'Hsp_qseq',
'Data' => shift @q_ex,
});
$self->element({'Name' => 'Hsp_hseq',
'Data' => shift @h_ex,
});
$self->element({'Name' => 'Hsp_midline',
'Data' => shift @m_ex,
});
## gc addition end
$self->element({'Name' => 'Hsp_score',
'Data' => $score});
$self->element({'Name' => 'Hsp_query-from',
'Data' => $qs});
$qs += $aln_len*$qstrand;
$self->element({'Name' => 'Hsp_query-to',
'Data' => $qs - ($qstrand*1)});
$hs += $deletes*$hstrand;
$self->element({'Name' => 'Hsp_hit-from',
'Data' => $hs});
$hs += $aln_len*$hstrand;
$self->element({'Name' => 'Hsp_hit-to',
'Data' => $hs -($hstrand*1)});
$self->element({'Name' => 'Hsp_align-len',
'Data' => $aln_len});
$self->element({'Name' => 'Hsp_identity',
'Data' => $aln_len - ($inserts + $deletes)});
$self->element({'Name' => 'Hsp_gaps',
'Data' => $inserts + $deletes});
$self->element({'Name' => 'Hsp_querygaps',
'Data' => $inserts});
$self->element({'Name' => 'Hsp_hitgaps',
'Data' => $deletes});
$self->end_element({'Name' => 'Hsp'});
$self->element({'Name' => 'Hit_score',
'Data' => $score});
$self->end_element({'Name' => 'Hit'});
$self->end_element({'Name' => 'ExonerateOutput'});
return $self->end_document();
} else {
# skipping this line
}
}
return $self->end_document() if( $seentop );
}
=head2 start_element
Title : start_element
Usage : $eventgenerator->start_element
Function: Handles a start element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
=cut
sub start_element{
my ($self,$data) = @_;
# we currently don't care about attributes
my $nm = $data->{'Name'};
my $type = $MODEMAP{$nm};
if( $type ) {
if( $self->_eventHandler->will_handle($type) ) {
my $func = sprintf("start_%s",lc $type);
$self->_eventHandler->$func($data->{'Attributes'});
}
unshift @{$self->{'_elements'}}, $type;
if($type eq 'result') {
$self->{'_values'} = {};
$self->{'_result'}= undef;
}
}
}
=head2 end_element
Title : start_element
Usage : $eventgenerator->end_element
Function: Handles an end element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
=cut
sub end_element {
my ($self,$data) = @_;
my $nm = $data->{'Name'};
my $type = $MODEMAP{$nm};
my $rc;
if( $type = $MODEMAP{$nm} ) {
if( $self->_eventHandler->will_handle($type) ) {
my $func = sprintf("end_%s",lc $type);
$rc = $self->_eventHandler->$func($self->{'_reporttype'},
$self->{'_values'});
}
shift @{$self->{'_elements'}};
} elsif( $MAPPING{$nm} ) {
if ( ref($MAPPING{$nm}) =~ /hash/i ) {
my $key = (keys %{$MAPPING{$nm}})[0];
$self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'};
} else {
$self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'};
}
} else {
$self->debug( "unknown nm $nm, ignoring\n");
}
$self->{'_last_data'} = ''; # remove read data if we are at
# end of an element
$self->{'_result'} = $rc if( defined $type && $type eq 'result' );
return $rc;
}
=head2 element
Title : element
Usage : $eventhandler->element({'Name' => $name, 'Data' => $str});
Function: Convience method that calls start_element, characters, end_element
Returns : none
Args : Hash ref with the keys 'Name' and 'Data'
=cut
sub element{
my ($self,$data) = @_;
$self->start_element($data);
$self->characters($data);
$self->end_element($data);
}
=head2 characters
Title : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
=cut
sub characters{
my ($self,$data) = @_;
return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ );
$self->{'_last_data'} = $data->{'Data'};
}
=head2 within_element
Title : within_element
Usage : if( $eventgenerator->within_element($element) ) {}
Function: Test if we are within a particular element
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
Args : string element name
=cut
sub within_element{
my ($self,$name) = @_;
return 0 if ( ! defined $name &&
! defined $self->{'_elements'} ||
scalar @{$self->{'_elements'}} == 0) ;
foreach ( @{$self->{'_elements'}} ) {
if( $_ eq $name ) {
return 1;
}
}
return 0;
}
=head2 in_element
Title : in_element
Usage : if( $eventgenerator->in_element($element) ) {}
Function: Test if we are in a particular element
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
Args : string element name
=cut
sub in_element{
my ($self,$name) = @_;
return 0 if ! defined $self->{'_elements'}->[0];
return ( $self->{'_elements'}->[0] eq $name)
}
=head2 start_document
Title : start_document
Usage : $eventgenerator->start_document
Function: Handle a start document event
Returns : none
Args : none
=cut
sub start_document{
my ($self) = @_;
$self->{'_lasttype'} = '';
$self->{'_values'} = {};
$self->{'_result'}= undef;
$self->{'_elements'} = [];
$self->{'_reporttype'} = 'exonerate';
}
=head2 end_document
Title : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none
=cut
sub end_document{
my ($self,@args) = @_;
return $self->{'_result'};
}
sub write_result {
my ($self, $blast, @args) = @_;
if( not defined($self->writer) ) {
$self->warn("Writer not defined. Using a $DEFAULT_WRITER_CLASS");
$self->writer( $DEFAULT_WRITER_CLASS->new() );
}
$self->SUPER::write_result( $blast, @args );
}
sub result_count {
my $self = shift;
return $self->{'_result_count'};
}
sub report_count { shift->result_count }
=head2 vulgar
Title : vulgar
Usage : $obj->vulgar($newval)
Function: Get/Set flag, do you want to build HSPs from VULGAR string?
Returns : value of vulgar (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub vulgar{
my $self = shift;
my $x = shift if @_;
if( @_ ) {
if( $_[0] && $self->{'_cigar'} ) {
$self->warn("Trying to set vulgar and cigar both to 1, must be either or");
$self->{'_cigar'} = 0;
return $self->{'_vulgar'} = 0;
}
}
return $self->{'_vulgar'};
}
=head2 cigar
Title : cigar
Usage : $obj->cigar($newval)
Function: Get/Set boolean flag do you want to build HSPs from CIGAR strings?
Returns : value of cigar (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub cigar{
my $self = shift;
my $x = shift if @_;
if( @_ ) {
if( $_[0] && $self->{'_vulgar'} ) {
$self->warn("Trying to set vulgar and cigar both to 1, must be either or");
$self->{'_vulgar'} = 0;
return $self->{'_cigar'} = 0;
}
}
return $self->{'_cigar'};
}
1;