#-----------------------------------------------------------------
#
# BioPerl module Bio::SearchIO::Writer::GbrowseGFF.pm
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Mark Wilkinson <markw@illuminae.com>
#
# You may distribute this module under the same terms as perl itself
#-----------------------------------------------------------------
=head1 NAME
Bio::SearchIO::Writer::GbrowseGFF - Interface for outputting parsed search results in Gbrowse GFF format
=head1 SYNOPSIS
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-file => 'result.blast',
-format => 'blast');
my $out = Bio::SearchIO->new(-output_format => 'GbrowseGFF',
-output_cigar => 1,
-output_signif => 1,
-file => ">result.gff");
while( my $r = $in->next_result ) {
$out->write_result($r);
}
=head1 DESCRIPTION
This writer produces Gbrowse flavour GFF from a Search::Result object.
=head1 AUTHOR Mark Wilkinson
Email markw-at-illuminae-dot-com
=head1 CONTRIBUTORS
Susan Miller sjmiller at email-DOT-arizon-DOT-edu
Jason Stajich jason at bioperl-dot-org
=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 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::SearchIO::Writer::GbrowseGFF;
use vars qw(%Defaults);
use strict;
$Defaults{'Prefix'} = 'EST';
$Defaults{'HSPTag'} = 'HSP';
$Defaults{'MatchTag'} = 'match';
use base qw(Bio::Root::Root Bio::SearchIO::SearchWriterI);
=head2 new
Title : new
Usage : my $obj = Bio::SearchIO::Writer::GbrowseGFF->new(@args);
Function: Builds a new Bio::SearchIO::Writer::GbrowseGFF object
Returns : an instance of Bio::SearchIO::Writer::GbrowseGFF
Args : -e_value => 10 : set e_value parsing cutoff (default undef)
(note the -e_value flag is deprecated.)
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
($self->{'_evalue'},
$self->{'_cigar'},
$self->{'_prefix'},
$self->{'_signif'} ) = $self->_rearrange([qw(E_VALUE OUTPUT_CIGAR PREFIX
OUTPUT_SIGNIF)], @args);
$self->{'_evalue'} && warn( "Use of the -e_value argument is deprecated.\nIn future, use \$writer->filter(\"type\", \&code) instead.\n\tparsing will proceed correctly with this e_value\n");
$self->{Gbrowse_HSPID} = 0;
$self->{Gbrowse_HITID} = 0;
$self->{'_prefix'} ||= $Defaults{'Prefix'};
return $self;
}
sub _incrementHSP {
my ($self) = @_;
return ++$self->{Gbrowse_HSPID};
}
sub _incrementHIT {
my ($self) = @_;
return ++$self->{Gbrowse_HITID}
}
# according to the GFF3 spec:
#"match". In addition to the generic "match"
#type, there are the subclasses "cDNA_match," "EST_match,"
#"translated_nucleotide_match," "nucleotide_to_protein_match," and
#"nucleotide_motif."
=head2 to_string
Purpose : Produce the Gbrowse format GFF lines for a Result
Usage : print $writer->to_string( $result_obj, @args);
Argument : $result_obj = A Bio::Search::Result::ResultI object
-version => 1|2|2.5|3 ; the GFF format you want to output (default 3)
-match_tag => match|cDNA_match|EST_match|translated_nucleotide_match
nucleotide_to_protein_match|nucleotide_motif
This is the SO term to be placed in GFF column 3.
-prefix => String to prefix the group by, default is EST
(see %Defaults class variable) A default can also
be set on object init
Returns : String containing data for each search Result or any of its
: sub-objects (Hits and HSPs).
Throws : n/a
=cut
#-reference => 'hit'|'query' ; whether the hit sequence name or the
# query sequence name is used as the
# 'reference' sequence (GFF column 1)
sub to_string {
my ($self, $result, @args) = @_;
my ($format, $reference,
$match_tag,$hsp_tag,
$prefix) = $self->_rearrange([qw
(VERSION
REFERENCE
MATCH_TAG HSP_TAG
PREFIX)], @args);
$self->warn($reference) if $reference;
$reference ||='hit'; # default is that the hit sequence (db sequence) becomes the reference sequence. I think this is fairly typical...
$match_tag ||= $Defaults{'MatchTag'}; # default is the generic 'match' tag.
$hsp_tag ||= $Defaults{'HSPTag'}; # default is the generic 'hsp' tag.
$prefix ||= $self->{'_prefix'};
$self->throw("$reference must be one of 'query', or 'hit'\n") unless $reference;
#************* THIS IS WHERE I STOPPED ****************
# *****************************************************
#*************************************************
$format ||='3';
my $gffio = Bio::Tools::GFF->new(-gff_version => $format); # try to set it
# just in case that behaviour changes (at the moment, an invalid format throws an exception, but it might return undef in the future
return "" unless defined $gffio; # be kind and don't return undef in case the person is putting the output directly into a print statement without testing it
# now $gffio is either false, or a valid GFF formatter
my ($GFF,$cigar,$score);
my ($resultfilter,$hitfilter,$hspfilter) = (
$self->filter('RESULT'),
$self->filter('HIT'),
$self->filter('HSP'));
$result->can('rewind') && $result->rewind(); # ensure we're at the beginning
next if (defined $resultfilter && ! (&{$resultfilter}($result)) );
while( my $hit = $result->next_hit ) {
if (defined $self->{_evalue}){
next unless ($hit->significance < $self->{_evalue});
}
next if( defined $hitfilter && ! &{$hitfilter}($hit) ); # test against filter code
my $refseq = $reference eq 'hit' ? $hit->name : $result->query_name;
my $seqname = $reference eq 'hit' ? $result->query_name : $hit->name; # hopefully this will be a simple identifier without a full description line!!
if ($self->{_signif}) {
$score = $hit->significance;
} else {
$score = $hit->raw_score;
}
$self->throw("No reference sequence name found in hit; required for GFF (this may not be your fault if your report type does not include reference sequence names)\n") unless $refseq;
my $source = $hit->algorithm;
$self->throw("No algorithm name found in hit; required for GFF (this may not be your fault if your report type does not include algorithm names)\n") unless $refseq;
$self->throw("This module only works on BLASTN reports at this time. Sorry.\n") unless $source eq "BLASTN";
my @plus_hsps;
my @minus_hsps;
# pre-process the HSP's because we later need to know
# the extents of the plus and munus strand
# on both the subject and query strands individually
my ($qpmin, $qpmax, $qmmin, $qmmax, $spmin, $spmax, $smmin, $smmax); # variables for the plus/minus strand min start and max end to know the full extents of the hit
while( my $hsp = $hit->next_hsp ) {
if ( defined $self->{_evalue} ) {
# for backward compatibility only
next unless ($hsp->significance < $self->{_evalue});
}
next if( defined $hspfilter && ! &{$hspfilter}($hsp) ); # test against HSP filter
if ($hsp->hit->strand >= 0 ){
push @plus_hsps, $hsp;
if (defined $qpmin){ # set or reset the minimum and maximum extent of the plus-strand hit
$qpmin = $hsp->query->start if $hsp->query->start < $qpmin;
$qpmax = $hsp->query->end if $hsp->query->end > $qpmax;
$spmin = $hsp->hit->start if $hsp->hit->start < $spmin;
$spmax = $hsp->hit->end if $hsp->hit->end > $spmax;
} else {
$qpmin = $hsp->query->start;
$qpmax = $hsp->query->end;
$spmin = $hsp->hit->start;
$spmax = $hsp->hit->end;
}
}
if ($hsp->hit->strand < 0 ){
push @minus_hsps, $hsp;
if (defined $qmmin){ # set or reset the minimum and maximum extent of the minus-strand hit
$qmmin = $hsp->query->start if $hsp->query->start < $qmmin;
$qmmax = $hsp->query->end if $hsp->query->end > $qmmax;
$smmin = $hsp->hit->start if $hsp->hit->start < $smmin;
$smmax = $hsp->hit->end if $hsp->hit->end > $smmax;
} else {
$qmmin = $hsp->query->start;
$qmmax = $hsp->query->end;
$smmin = $hsp->hit->start;
$smmax = $hsp->hit->end;
}
}
#else next if there is no strand, but that makes no sense..??
}
next unless (scalar(@plus_hsps) + scalar(@minus_hsps)); # next if no hsps (??)
my $ID = $self->_incrementHIT();
# okay, write out the index line for the entire hit before
# processing HSP's
# unfortunately (or not??), HitI objects do not implement
# SeqFeatureI, so we can't just call ->gff_string
# as a result, this module is quite brittle to changes
# in the GFF format since we are hard-coding the GFF output here :-(
if (scalar(@plus_hsps)){
my %tags = ( 'ID' => "match_sequence$ID");
if ($format==2.5) {
$tags{'Target'} = "$prefix:$seqname";
$tags{'tstart'} = $qmmin;
$tags{'tend'} = $qmmax;
} else {
$tags{'Target'} = "$prefix:$seqname $qpmin $qpmax";
}
if ( $self->{'_cigar'} ) {
$tags{'Gap'} = $cigar;
}
my $feat = Bio::SeqFeature::Generic->new(
-seq_id => $refseq,
-source_tag => $source,
-primary_tag => $match_tag,
-start => $spmin,
-end => $spmax,
-score => $score,
-strand => '+',
-frame => '.',
-tag => \%tags
);
my $formatter = Bio::Tools::GFF->new(-gff_version => $format);
$GFF .= $feat->gff_string($formatter)."\n";
}
if (scalar(@minus_hsps)){
my %tags = ( 'ID' => "match_sequence$ID");
if ($format==2.5) {
$tags{'Target'} = "$prefix:$seqname";
$tags{'tstart'} = $qpmax;
$tags{'tend'} = $qpmin;
}
else {
$tags{'Target'} = "$prefix:$seqname $qpmax $qpmin";
}
my $feat = Bio::SeqFeature::Generic->new(
-seq_id => $refseq,
-source_tag => $source,
-primary_tag => $match_tag,
-start => $smmin,
-end => $smmax,
-score => $score,
-strand => '-',
-frame => '.',
-tag => \%tags
);
my $formatter = Bio::Tools::GFF->new(-gff_version => $format);
$GFF .= $feat->gff_string($formatter)."\n";
}
# process + strand hsps
foreach my $hsp (@plus_hsps){
my $hspID = $self->_incrementHSP();
my $qstart = $hsp->query->start;
my $qend = $hsp->query->end;
my $sstart = $hsp->hit->start;
my $send = $hsp->hit->end;
my $score = $hsp->score;
my %tags = ( 'ID' => "match_hsp$hspID",
'Parent' => "match_sequence$ID" );
if ($format==2.5) {
$tags{'Target'} = "$prefix:$seqname";
$tags{'tstart'} = $qstart;
$tags{'tend'} = $qend;
}
else {
$tags{'Target'} = "$prefix:$seqname $qstart $qend";
}
if ( $self->{'_cigar'} ) {
$tags{'Gap'} = $hsp->cigar_string;
}
my $feat = Bio::SeqFeature::Generic->new(
-seq_id => $refseq,
-source_tag => $source,
-primary_tag => $hsp_tag,
-start => $sstart,
-end => $send,
-score => $score,
-strand => '+',
-frame => '.',
-tag => \%tags
);
my $formatter = Bio::Tools::GFF->new(-gff_version => $format);
$GFF .= $feat->gff_string($formatter)."\n";
}
foreach my $hsp (@minus_hsps) {
my $hspID = $self->_incrementHSP();
my $qstart = $hsp->query->start;
my $qend = $hsp->query->end;
my $sstart = $hsp->hit->start;
my $send = $hsp->hit->end;
my $score = $hsp->score;
my %tags = ( 'ID' => "match_hsp$hspID",
'Parent' => "match_sequence$ID" );
if ($format==2.5) {
$tags{'Target'} = "$prefix:$seqname";
$tags{'tstart'} = $qend;
$tags{'tend'} = $qstart;
}
else {
$tags{'Target'} = "$prefix:$seqname $qend $qstart";
}
if ( $self->{'_cigar'} ) {
$tags{'Gap'} = $hsp->cigar_string;
}
my $feat = Bio::SeqFeature::Generic->new(
-seq_id => $refseq,
-source_tag => $source,
-primary_tag => $hsp_tag,
-start => $sstart,
-end => $send,
-score => $score,
-strand => '-',
-frame => '.',
-tag => \%tags
);
my $formatter = Bio::Tools::GFF->new(-gff_version => $format);
$GFF .= $feat->gff_string($formatter) ."\n";
}
}
return $GFF;
}
sub significance_filter {
my ($self,$method,$code) = @_;
return unless $method;
$method = uc($method);
if( $method ne 'HSP' &&
$method ne 'HIT' &&
$method ne 'RESULT' ) {
$self->warn("Unknown method $method");
return;
}
if( $code ) {
$self->throw("Must provide a valid code reference") unless ref($code) =~ /CODE/;
$self->{$method} = $code;
}
return $self->{$method};
}
=head2 start_report
Title : start_report
Usage : $self->start_report()
Function: has no function, returns nothing
Returns : empty string
Args : none
=cut
sub start_report { return '' }
=head2 end_report
Title : end_report
Usage : $self->end_report()
Function: has no function, returns nothing
Returns : empty string
Args : none
=cut
sub end_report { return '' }
=head2 filter
Title : filter
Usage : $writer->filter('hsp', \&hsp_filter);
Function: Filter out either at HSP,Hit,or Result level
Returns : none
Args : string => data type,
CODE reference
Note : GbrowseGFF.pm makes no changes to the default filter code
=cut
1;