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# BioPerl module for Bio::SearchIO::sim4
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# Cared for by Jason Stajich <jason-at-bioperl-dot-org>
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# Copyright Jason Stajich
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# You may distribute this module under the same terms as perl itself
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# POD documentation - main docs before the code
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Bio::SearchIO::sim4 - parser for Sim4 alignments
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# do not use this module directly, it is a driver for SearchIO
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my $searchio = new Bio::SearchIO(-file => 'results.sim4',
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while ( my $result = $searchio->next_result ) {
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while ( my $hit = $result->next_hit ) {
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while ( my $hsp = $hit->next_hsp ) {
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This is a driver for the SearchIO system for parsing Sim4.
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http://globin.cse.psu.edu/html/docs/sim4.html
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User feedback is an integral part of the evolution of this and other
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Bioperl modules. Send your comments and suggestions preferably to
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the Bioperl mailing list. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/MailList.shtml - About the mailing lists
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Report bugs to the Bioperl bug tracking system to help us keep track
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of the bugs and their resolution. Bug reports can be submitted via
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bioperl-bugs@bioperl.org
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http://bioperl.org/bioperl-bugs/
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=head1 AUTHOR - Jason Stajich
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Email jason-at-bioperl-dot-org
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Luc Gauthier (lgauthie@hotmail.com)
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The rest of the documentation details each of the object methods.
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Internal methods are usually preceded with a _
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# Let the code begin...
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package Bio::SearchIO::sim4;
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use vars qw(@ISA $DEFAULTFORMAT %ALIGN_TYPES
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%MAPPING %MODEMAP $DEFAULT_WRITER_CLASS);
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use Bio::SearchIO::SearchResultEventBuilder;
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@ISA = qw(Bio::SearchIO );
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$DEFAULTFORMAT = 'SIM4';
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$DEFAULT_WRITER_CLASS = 'Bio::Search::Writer::HitTableWriter';
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'Sim4Output' => 'result',
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'Hsp_query-from'=> 'HSP-query_start',
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'Hsp_query-to' => 'HSP-query_end',
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'Hsp_qseq' => 'HSP-query_seq',
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'Hsp_qlength' => 'HSP-query_length',
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'Hsp_querygaps' => 'HSP-query_gaps',
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'Hsp_hit-from' => 'HSP-hit_start',
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'Hsp_hit-to' => 'HSP-hit_end',
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'Hsp_hseq' => 'HSP-hit_seq',
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'Hsp_hlength' => 'HSP-hit_length',
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'Hsp_hitgaps' => 'HSP-hit_gaps',
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'Hsp_midline' => 'HSP-homology_seq',
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'Hsp_score' => 'HSP-score',
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'Hsp_align-len' => 'HSP-hsp_length',
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'Hsp_identity' => 'HSP-identical',
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'Hit_id' => 'HIT-name',
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'Hit_desc' => 'HIT-description',
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'Hit_len' => 'HIT-length',
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'Sim4Output_program' => 'RESULT-algorithm_name',
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'Sim4Output_query-def' => 'RESULT-query_name',
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'Sim4Output_query-desc'=> 'RESULT-query_description',
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'Sim4Output_query-len' => 'RESULT-query_length',
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Usage : my $obj = new Bio::SearchIO::sim4();
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Function: Builds a new Bio::SearchIO::sim4 object
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Returns : an instance of Bio::SearchIO::sim4
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Usage : my $result = $searchio->next_result;
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Function: Returns the next Result from a search
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Returns : Bio::Search::Result::ResultI object
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# Declare/adjust needed variables
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$self->{'_last_data'} = '';
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my ($seentop, $qfull, @hsps, %alignment, $format);
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my $hit_direction = 1;
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# Start document and main element
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$self->start_document();
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$self->start_element({'Name' => 'Sim4Output'});
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# Read output report until EOF
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while( defined($_ = $self->_readline) ) {
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# Skip empty lines, chomp filled ones
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next if( /^\s+$/); chomp;
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# Make sure sim4 output format is not 2 or 5
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if ( /^#:lav/ ) { $format = 2; }
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elsif ( /^<|>/ ) { $format = 5; }
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$self->throw("Bio::SearchIO::sim4 module cannot parse 'type $format' outputs.") if $format;
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# This line indicates the start of a new hit
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if( /^seq1\s*=\s*(\S+),\s+(\d+)/ ) {
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# First hit? Adjust some parameters if so
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$self->element( {'Name' => 'Sim4Output_query-def',
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$self->element( {'Name' => 'Sim4Output_query-len',
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# A previous HSP may need to be ended
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$self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') );
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# A previous hit exists? End it and reset needed variables
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if ( $self->in_element('hit') ) {
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$self->start_element({'Name' => 'Hsp'});
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while (my ($name, $data) = each %$_) {
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$self->{'_currentHSP'}{$name} = $data;
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$self->end_element({'Name' => 'Hsp'});
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$self->{'_currentHSP'} = {};
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$format = 0 if @hsps;
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$self->end_element({'Name' => 'Hit'});
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# This line describes the current hit... so let's start it
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} elsif( /^seq2\s*=\s*(\S+)\s+\(>?(\S+)\s*\),\s*(\d+)/ ) {
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$self->start_element({'Name' => 'Hit'});
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$self->element( {'Name' => 'Hit_id', 'Data' => $2} );
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$self->element( {'Name' => 'Hit_desc', 'Data' => $1} );
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$self->element( {'Name' => 'Hit_len', 'Data' => $3} );
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# This line may give additional details about query or subject
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} elsif( /^>(\S+)\s*(.*)?/ ) {
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# Previous line was query details... this time subject details
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$format = 4 if !$format;
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$self->element({'Name' => 'Hit_desc', 'Data' => $2});
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# First line of this type is always query details for a given hit
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$self->element({'Name' => 'Sim4Output_query-desc', 'Data' => $2});
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# This line indicates that subject is on reverse strand
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} elsif( /^\(complement\)/ ) {
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# This line describes the current HSP... so add it to @hsps array
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} elsif( /^\(?(\d+)\-(\d+)\)?\s+\(?(\d+)\-(\d+)\)?\s+(\d+)/ ) {
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my ($qs,$qe,$hs,$he,$pid) = ($1,$2,$3,$4,$5);
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'Hsp_query-from' => $qs,
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'Hsp_query-to' => $qe,
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'Hsp_hit-from' => $hit_direction >= 0 ? $hs : $he,
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'Hsp_hit-to' => $hit_direction >= 0 ? $he : $hs,
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'Hsp_identity' => 0, #can't determine correctly from raw pct
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'Hsp_qlength' => abs($qe - $qs) + 1,
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'Hsp_hlength' => abs($he - $hs) + 1,
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'Hsp_align-len' => abs($qe - $qs) + 1,
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# This line indicates the start of an alignment block
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} elsif( /^\s+(\d+)\s/ ) {
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# Store the current alignment block in a hash
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for( my $i = 0; defined($_) && $i < 4; $i++ ) {
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my ($start, $string) = /^\s+(\d*)\s(.*)/;
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$alignment{$ALIGN_TYPES{$i}} = { start => $start, string => $i != 2
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: (' ' x (length($alignment{$ALIGN_TYPES{$i-1}}{string}) - length($string))) . $string
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$_ = $self->_readline();
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# 'Ruler' line indicates the start of a new HSP
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if ($alignment{Ruler}{start} == 0) {
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$format = @hsps ? 3 : 1 if !$format;
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# A previous HSP may need to be ended
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$self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') );
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# Start the new HSP and fill the '_currentHSP' property with available details
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$self->start_element({'Name' => 'Hsp'});
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$self->{'_currentHSP'} = @hsps ? shift @hsps : {
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'Hsp_query-from' => $alignment{Query}{start},
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'Hsp_hit-from' => $alignment{Sbjct}{start},
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# Midline indicates a boundary between two HSPs
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if ( $alignment{Mid}{string} =~ /<|>/g ) {
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my ($hsp_start, $hsp_end);
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# Are we currently in an open HSP?
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if ( $self->in_element('hsp') ) {
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# Find end pos, adjust 'gaps', 'seq' and 'midline' properties... then close HSP
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$hsp_end = (pos $alignment{Mid}{string}) - 1;
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$self->{'_currentHSP'}{'Hsp_querygaps'} +=
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($self->{'_currentHSP'}{'Hsp_qseq'} .= substr($alignment{Query}{string}, 0, $hsp_end)) =~ s/ /-/g;
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$self->{'_currentHSP'}{'Hsp_hitgaps'} +=
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($self->{'_currentHSP'}{'Hsp_hseq'} .= substr($alignment{Sbjct}{string}, 0, $hsp_end)) =~ s/ /-/g;
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($self->{'_currentHSP'}{'Hsp_midline'} .= substr($alignment{Mid}{string}, 0, $hsp_end)) =~ s/-/ /g;
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$self->end_element({'Name' => 'Hsp'});
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# Does a new HSP start in the current alignment block?
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if ( $alignment{Mid}{string} =~ /\|/g ) {
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# Find start pos, start new HSP and fill it with available details
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$hsp_start = (pos $alignment{Mid}{string}) - 1;
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$self->start_element({'Name' => 'Hsp'});
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$self->{'_currentHSP'} = @hsps ? shift @hsps : {};
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$self->{'_currentHSP'}{'Hsp_querygaps'} +=
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($self->{'_currentHSP'}{'Hsp_qseq'} = substr($alignment{Query}{string}, $hsp_start)) =~ s/ /-/g;
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$self->{'_currentHSP'}{'Hsp_hitgaps'} +=
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($self->{'_currentHSP'}{'Hsp_hseq'} = substr($alignment{Sbjct}{string}, $hsp_start)) =~ s/ /-/g;
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($self->{'_currentHSP'}{'Hsp_midline'} = substr($alignment{Mid}{string}, $hsp_start)) =~ s/-/ /g;
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# No HSP is currently open...
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# Find start pos, start new HSP and fill it with available
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# details then skip to next alignment block
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$hsp_start = index($alignment{Mid}{string}, '|');
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$self->start_element({'Name' => 'Hsp'});
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$self->{'_currentHSP'} = @hsps ? shift @hsps : {
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'Hsp_query-from' => $alignment{Query}{start},
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$self->{'_currentHSP'}{'Hsp_querygaps'} +=
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($self->{'_currentHSP'}{'Hsp_qseq'} = substr($alignment{Query}{string}, $hsp_start)) =~ s/ /-/g;
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$self->{'_currentHSP'}{'Hsp_hitgaps'} +=
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($self->{'_currentHSP'}{'Hsp_hseq'} = substr($alignment{Sbjct}{string}, $hsp_start)) =~ s/ /-/g;
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($self->{'_currentHSP'}{'Hsp_midline'} = substr($alignment{Mid}{string}, $hsp_start)) =~ s/-/ /g;
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# Current alignment block does not contain HSPs boundary
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# We only need to adjust details of the current HSP
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$self->{'_currentHSP'}{'Hsp_query-from'} ||=
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$alignment{Query}{start} -
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length($self->{'_currentHSP'}{'Hsp_qseq'} || '');
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$self->{'_currentHSP'}{'Hsp_hit-from'} ||=
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$alignment{Sbjct}{start} -
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length($self->{'_currentHSP'}{'Hsp_hseq'} || '');
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$self->{'_currentHSP'}{'Hsp_querygaps'} +=
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($self->{'_currentHSP'}{'Hsp_qseq'} .=
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$alignment{Query}{string}) =~ s/ /-/g;
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$self->{'_currentHSP'}{'Hsp_hitgaps'} +=
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($self->{'_currentHSP'}{'Hsp_hseq'} .=
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$alignment{Sbjct}{string}) =~ s/ /-/g;
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($self->{'_currentHSP'}{'Hsp_midline'} .=
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$alignment{Mid}{string}) =~ s/-/ /g;
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# We are done reading the sim4 report, end everything and return
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$self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') );
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if ( $self->in_element('hit') ) {
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$self->start_element({'Name' => 'Hsp'});
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while (my ($name, $data) = each %$_) {
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$self->{'_currentHSP'}{$name} = $data;
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$self->end_element({'Name' => 'Hsp'});
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$self->end_element({'Name' => 'Hit'});
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# adjust result's algorithm name, end output and return
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$self->element({'Name' => 'Sim4Output_program',
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'Data' => $DEFAULTFORMAT . ' (A=' . (defined $format ? $format : '?') . ')'});
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$self->end_element({'Name' => 'Sim4Output'});
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return $self->end_document();
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Title : start_element
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Usage : $eventgenerator->start_element
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Function: Handles a start element event
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Args : hashref with at least 2 keys 'Data' and 'Name'
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my ($self,$data) = @_;
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# we currently don't care about attributes
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my $nm = $data->{'Name'};
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my $type = $MODEMAP{$nm};
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if( $self->_will_handle($type) ) {
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my $func = sprintf("start_%s",lc $type);
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$self->_eventHandler->$func($data->{'Attributes'});
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unshift @{$self->{'_elements'}}, $type;
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if($type eq 'result') {
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$self->{'_values'} = {};
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$self->{'_result'}= undef;
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Title : start_element
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Usage : $eventgenerator->end_element
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Function: Handles an end element event
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Args : hashref with at least 2 keys 'Data' and 'Name'
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my ($self,$data) = @_;
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my $nm = $data->{'Name'};
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my $type = $MODEMAP{$nm};
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$self->{'_currentHSP'}{'Hsp_midline'} ||= '';
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$self->{'_currentHSP'}{'Hsp_query-to'} ||=
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$self->{'_currentHSP'}{'Hsp_query-from'} + length($self->{'_currentHSP'}{'Hsp_qseq'}) - 1 - $self->{'_currentHSP'}{'Hsp_querygaps'};
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$self->{'_currentHSP'}{'Hsp_hit-to'} ||=
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$self->{'_currentHSP'}{'Hsp_hit-from'} + length($self->{'_currentHSP'}{'Hsp_hseq'}) - 1 - $self->{'_currentHSP'}{'Hsp_hitgaps'};
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$self->{'_currentHSP'}{'Hsp_identity'} ||=
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($self->{'_currentHSP'}{'Hsp_midline'} =~ tr/\|//);
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$self->{'_currentHSP'}{'Hsp_qlength'} ||= abs($self->{'_currentHSP'}{'Hsp_query-to'} - $self->{'_currentHSP'}{'Hsp_query-from'}) + 1;
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$self->{'_currentHSP'}{'Hsp_hlength'} ||= abs($self->{'_currentHSP'}{'Hsp_hit-to'} - $self->{'_currentHSP'}{'Hsp_hit-from'}) + 1;
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$self->{'_currentHSP'}{'Hsp_align-len'} ||= abs($self->{'_currentHSP'}{'Hsp_query-to'} - $self->{'_currentHSP'}{'Hsp_query-from'}) + 1;
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$self->{'_currentHSP'}{'Hsp_score'} ||= int(100 * ($self->{'_currentHSP'}{'Hsp_identity'} / $self->{'_currentHSP'}{'Hsp_align-len'}));
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foreach (keys %{$self->{'_currentHSP'}}) {
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$self->element({'Name' => $_, 'Data' => delete ${$self->{'_currentHSP'}}{$_}});
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if( $type = $MODEMAP{$nm} ) {
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if( $self->_will_handle($type) ) {
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my $func = sprintf("end_%s",lc $type);
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$rc = $self->_eventHandler->$func($self->{'_reporttype'},
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shift @{$self->{'_elements'}};
433
} elsif( $MAPPING{$nm} ) {
435
if ( ref($MAPPING{$nm}) =~ /hash/i ) {
436
my $key = (keys %{$MAPPING{$nm}})[0];
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$self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'};
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$self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'};
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$self->debug( "unknown nm $nm, ignoring\n");
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$self->{'_last_data'} = ''; # remove read data if we are at
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$self->{'_result'} = $rc if( defined $type && $type eq 'result' );
453
Usage : $eventhandler->element({'Name' => $name, 'Data' => $str});
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Function: Convience method that calls start_element, characters, end_element
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Args : Hash ref with the keys 'Name' and 'Data'
462
my ($self,$data) = @_;
463
$self->start_element($data);
464
$self->characters($data);
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$self->end_element($data);
471
Usage : $eventgenerator->characters($str)
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Function: Send a character events
480
my ($self,$data) = @_;
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return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ );
483
if( $self->in_element('hsp') &&
484
$data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) {
485
$self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'};
488
$self->{'_last_data'} = $data->{'Data'};
491
=head2 within_element
493
Title : within_element
494
Usage : if( $eventgenerator->within_element($element) ) {}
495
Function: Test if we are within a particular element
496
This is different than 'in' because within can be tested
499
Args : string element name
505
my ($self,$name) = @_;
506
return 0 if ( ! defined $name &&
507
! defined $self->{'_elements'} ||
508
scalar @{$self->{'_elements'}} == 0) ;
509
foreach ( @{$self->{'_elements'}} ) {
521
Usage : if( $eventgenerator->in_element($element) ) {}
522
Function: Test if we are in a particular element
523
This is different than 'in' because within can be tested
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Args : string element name
532
my ($self,$name) = @_;
533
return 0 if ! defined $self->{'_elements'}->[0];
534
return ( $self->{'_elements'}->[0] eq $name)
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=head2 start_document
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Title : start_document
540
Usage : $eventgenerator->start_document
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Function: Handle a start document event
550
$self->{'_lasttype'} = '';
551
$self->{'_values'} = {};
552
$self->{'_result'}= undef;
553
$self->{'_elements'} = [];
554
$self->{'_reporttype'} = $DEFAULTFORMAT;
561
Usage : $eventgenerator->end_document
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Function: Handles an end document event
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Returns : Bio::Search::Result::ResultI object
570
my ($self,@args) = @_;
571
return $self->{'_result'};
576
my ($self, $blast, @args) = @_;
578
if( not defined($self->writer) ) {
579
$self->warn("Writer not defined. Using a $DEFAULT_WRITER_CLASS");
580
$self->writer( $DEFAULT_WRITER_CLASS->new() );
582
$self->SUPER::write_result( $blast, @args );
586
return 1; # can a sim4 report contain more than one result?
589
sub report_count { shift->result_count }
594
Usage : Private method. For internal use only.
595
if( $self->_will_handle($type) ) { ... }
596
Function: Provides an optimized way to check whether or not an element of a
597
given type is to be handled.
598
Returns : Reference to EventHandler object if the element type is to be handled.
599
undef if the element type is not to be handled.
600
Args : string containing type of element.
604
1. Using the cached pointer to the EventHandler to minimize repeated lookups.
605
2. Caching the will_handle status for each type that is encountered
606
so that it only need be checked by calling handler->will_handle($type) once.
608
This does not lead to a major savings by itself (only 5-10%).
609
In combination with other optimizations, or for large parse jobs, the
610
savings good be significant.
612
To test against the unoptimized version, remove the parentheses from
613
around the third term in the ternary " ? : " operator and add two
614
calls to $self-E<gt>_eventHandler().
619
my ($self,$type) = @_;
620
my $handler = $self->{'_handler_cache'} ||= $self->_eventHandler;
622
my $will_handle = defined($self->{'_will_handle_cache'}->{$type})
623
? $self->{'_will_handle_cache'}->{$type}
624
: ($self->{'_will_handle_cache'}->{$type} =
625
$handler->will_handle($type));
627
return $will_handle ? $handler : undef;
added
removed
Bio/SearchIO/sim4.pm
