# $Id: sim4.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::SearchIO::sim4 # # Please direct questions and support issues to # # Cared for by Jason Stajich # # 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::sim4 - parser for Sim4 alignments =head1 SYNOPSIS # do not use this module directly, it is a driver for SearchIO use Bio::SearchIO; my $searchio = Bio::SearchIO->new(-file => 'results.sim4', -format => 'sim4'); while ( my $result = $searchio->next_result ) { while ( my $hit = $result->next_hit ) { while ( my $hsp = $hit->next_hsp ) { # ... } } } =head1 DESCRIPTION This is a driver for the SearchIO system for parsing Sim4. http://globin.cse.psu.edu/html/docs/sim4.html Cannot parse LAV or 'exon file' formats (A=2 or A=5) =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.open-bio.org/ =head1 AUTHOR - Jason Stajich Email jason-at-bioperl-dot-org =head1 CONTRIBUTORS Luc Gauthier (lgauthie@hotmail.com) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SearchIO::sim4; use strict; use vars qw($DEFAULTFORMAT %ALIGN_TYPES %MAPPING %MODEMAP $DEFAULT_WRITER_CLASS); use POSIX; use Bio::SearchIO::SearchResultEventBuilder; use base qw(Bio::SearchIO); $DEFAULTFORMAT = 'SIM4'; $DEFAULT_WRITER_CLASS = 'Bio::Search::Writer::HitTableWriter'; %ALIGN_TYPES = ( 0 => 'Ruler', 1 => 'Query', 2 => 'Mid', 3 => 'Sbjct' ); %MODEMAP = ( 'Sim4Output' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); %MAPPING = ( 'Hsp_query-from'=> 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_qlength' => 'HSP-query_length', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_hlength' => 'HSP-hit_length', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_score' => 'HSP-score', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_identity' => 'HSP-identical', 'Hit_id' => 'HIT-name', 'Hit_desc' => 'HIT-description', 'Hit_len' => 'HIT-length', 'Sim4Output_program' => 'RESULT-algorithm_name', 'Sim4Output_query-def' => 'RESULT-query_name', 'Sim4Output_query-desc'=> 'RESULT-query_description', 'Sim4Output_query-len' => 'RESULT-query_length', ); =head2 new Title : new Usage : my $obj = Bio::SearchIO::sim4->new(); Function: Builds a new Bio::SearchIO::sim4 object Returns : an instance of Bio::SearchIO::sim4 Args : =cut =head2 next_result Title : next_result Usage : my $result = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none =cut sub next_result { my ($self) = @_; local $/ = "\n"; local $_; # Declare/adjust needed variables $self->{'_last_data'} = ''; my ($seentop, $qfull, @hsps, %alignment, $format); my $hit_direction = 1; # Start document and main element $self->start_document(); $self->start_element({'Name' => 'Sim4Output'}); my $lastquery = ''; # Read output report until EOF while( defined($_ = $self->_readline) ) { # Skip empty lines, chomp filled ones next if( /^\s+$/); chomp; # Make sure sim4 output format is not 2 or 5 if (!$seentop) { if ( /^\#:lav/ ) { $format = 2; } elsif ( /^<|>/ ) { $format = 5; } $self->throw("Bio::SearchIO::sim4 module cannot parse 'type $format' outputs.") if $format; } # This line indicates the start of a new hit if( /^seq1\s*=\s*(\S+),\s+(\d+)/ ) { my ($nm,$desc) = ($1,$2); # First hit? Adjust some parameters if so if ( ! $seentop ) { $self->element( {'Name' => 'Sim4Output_query-def', 'Data' => $nm} ); $self->element( {'Name' => 'Sim4Output_query-len', 'Data' => $desc} ); $seentop = 1; } elsif( $nm ne $lastquery ) { $self->_pushback($_); last; } $lastquery = $nm; # A previous HSP may need to be ended $self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') ); # A previous hit exists? End it and reset needed variables if ( $self->in_element('hit') ) { foreach (@hsps) { $self->start_element({'Name' => 'Hsp'}); while (my ($name, $data) = each %$_) { $self->{'_currentHSP'}{$name} = $data; } $self->end_element({'Name' => 'Hsp'}); $self->{'_currentHSP'} = {}; } $format = 0 if @hsps; @hsps = (); %alignment = (); $qfull = 0; $hit_direction = 1; $self->end_element({'Name' => 'Hit'}); } # This line describes the current hit... so let's start it } elsif( /^seq2\s*=\s*(\S+)\s+\(>?(\S+)\s*\),\s*(\d+)/ ) { $self->start_element({'Name' => 'Hit'}); $self->element( {'Name' => 'Hit_id', 'Data' => $2} ); $self->element( {'Name' => 'Hit_desc', 'Data' => $1} ); $self->element( {'Name' => 'Hit_len', 'Data' => $3} ); # This line may give additional details about query or subject } elsif( /^>(\S+)\s*(.*)?/ ) { # Previous line was query details... this time subject details if( $qfull ) { $format = 4 if !$format; $self->element({'Name' => 'Hit_desc', 'Data' => $2}); # First line of this type is always query details for a given hit } else { $self->element({'Name' => 'Sim4Output_query-desc', 'Data' => $2}); $qfull = 1; } # This line indicates that subject is on reverse strand } elsif( /^\(complement\)/ ) { $hit_direction = -1; # This line describes the current HSP... so add it to @hsps array } elsif( /^\(?(\d+)\-(\d+)\)?\s+\(?(\d+)\-(\d+)\)?\s+(\d+)/ ) { my ($qs,$qe,$hs,$he,$pid) = ($1,$2,$3,$4,$5); push @hsps, { 'Hsp_query-from' => $qs, 'Hsp_query-to' => $qe, 'Hsp_hit-from' => $hit_direction >= 0 ? $hs : $he, 'Hsp_hit-to' => $hit_direction >= 0 ? $he : $hs, 'Hsp_identity' => 0, #can't determine correctly from raw pct 'Hsp_qlength' => abs($qe - $qs) + 1, 'Hsp_hlength' => abs($he - $hs) + 1, 'Hsp_align-len' => abs($qe - $qs) + 1, }; # This line indicates the start of an alignment block } elsif( /^\s+(\d+)\s/ ) { # Store the current alignment block in a hash for( my $i = 0; defined($_) && $i < 4; $i++ ) { my ($start, $string) = /^\s+(\d*)\s(.*)/; $alignment{$ALIGN_TYPES{$i}} = { start => $start, string => $i != 2 ? $string : (' ' x (length($alignment{$ALIGN_TYPES{$i-1}}{string}) - length($string))) . $string }; $_ = $self->_readline(); } # 'Ruler' line indicates the start of a new HSP if ($alignment{Ruler}{start} == 0) { $format = @hsps ? 3 : 1 if !$format; # A previous HSP may need to be ended $self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') ); # Start the new HSP and fill the '_currentHSP' property with available details $self->start_element({'Name' => 'Hsp'}); $self->{'_currentHSP'} = @hsps ? shift @hsps : { 'Hsp_query-from' => $alignment{Query}{start}, 'Hsp_hit-from' => $alignment{Sbjct}{start}, } } # Midline indicates a boundary between two HSPs if ( $alignment{Mid}{string} =~ /<|>/g ) { my ($hsp_start, $hsp_end); # Are we currently in an open HSP? if ( $self->in_element('hsp') ) { # Find end pos, adjust 'gaps', 'seq' and 'midline' properties... then close HSP $hsp_end = (pos $alignment{Mid}{string}) - 1; $self->{'_currentHSP'}{'Hsp_querygaps'} += ($self->{'_currentHSP'}{'Hsp_qseq'} .= substr($alignment{Query}{string}, 0, $hsp_end)) =~ s/ /-/g; $self->{'_currentHSP'}{'Hsp_hitgaps'} += ($self->{'_currentHSP'}{'Hsp_hseq'} .= substr($alignment{Sbjct}{string}, 0, $hsp_end)) =~ s/ /-/g; ($self->{'_currentHSP'}{'Hsp_midline'} .= substr($alignment{Mid}{string}, 0, $hsp_end)) =~ s/-/ /g; $self->end_element({'Name' => 'Hsp'}); # Does a new HSP start in the current alignment block? if ( $alignment{Mid}{string} =~ /\|/g ) { # Find start pos, start new HSP and fill it with available details $hsp_start = (pos $alignment{Mid}{string}) - 1; $self->start_element({'Name' => 'Hsp'}); $self->{'_currentHSP'} = @hsps ? shift @hsps : {}; $self->{'_currentHSP'}{'Hsp_querygaps'} += ($self->{'_currentHSP'}{'Hsp_qseq'} = substr($alignment{Query}{string}, $hsp_start)) =~ s/ /-/g; $self->{'_currentHSP'}{'Hsp_hitgaps'} += ($self->{'_currentHSP'}{'Hsp_hseq'} = substr($alignment{Sbjct}{string}, $hsp_start)) =~ s/ /-/g; ($self->{'_currentHSP'}{'Hsp_midline'} = substr($alignment{Mid}{string}, $hsp_start)) =~ s/-/ /g; } } # No HSP is currently open... else { # Find start pos, start new HSP and fill it with available # details then skip to next alignment block $hsp_start = index($alignment{Mid}{string}, '|'); $self->start_element({'Name' => 'Hsp'}); $self->{'_currentHSP'} = @hsps ? shift @hsps : { 'Hsp_query-from' => $alignment{Query}{start}, }; $self->{'_currentHSP'}{'Hsp_querygaps'} += ($self->{'_currentHSP'}{'Hsp_qseq'} = substr($alignment{Query}{string}, $hsp_start)) =~ s/ /-/g; $self->{'_currentHSP'}{'Hsp_hitgaps'} += ($self->{'_currentHSP'}{'Hsp_hseq'} = substr($alignment{Sbjct}{string}, $hsp_start)) =~ s/ /-/g; ($self->{'_currentHSP'}{'Hsp_midline'} = substr($alignment{Mid}{string}, $hsp_start)) =~ s/-/ /g; next; } } # Current alignment block does not contain HSPs boundary else { # Start a new HSP if none is currently open # (Happens if last boundary finished at the very end of previous block) if ( !$self->in_element('hsp') ) { $self->start_element({'Name' => 'Hsp'}); $self->{'_currentHSP'} = @hsps ? shift @hsps : { 'Hsp_query-from' => $alignment{Query}{start}, 'Hsp_hit-from' => $alignment{Sbjct}{start}, } } # Adjust details of the current HSP $self->{'_currentHSP'}{'Hsp_query-from'} ||= $alignment{Query}{start} - length($self->{'_currentHSP'}{'Hsp_qseq'} || ''); $self->{'_currentHSP'}{'Hsp_hit-from'} ||= $alignment{Sbjct}{start} - length($self->{'_currentHSP'}{'Hsp_hseq'} || ''); $self->{'_currentHSP'}{'Hsp_querygaps'} += ($self->{'_currentHSP'}{'Hsp_qseq'} .= $alignment{Query}{string}) =~ s/ /-/g; $self->{'_currentHSP'}{'Hsp_hitgaps'} += ($self->{'_currentHSP'}{'Hsp_hseq'} .= $alignment{Sbjct}{string}) =~ s/ /-/g; ($self->{'_currentHSP'}{'Hsp_midline'} .= $alignment{Mid}{string}) =~ s/-/ /g; } } } # We are done reading the sim4 report, end everything and return if( $seentop ) { # end HSP if needed $self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') ); # end Hit if needed if ( $self->in_element('hit') ) { foreach (@hsps) { $self->start_element({'Name' => 'Hsp'}); while (my ($name, $data) = each %$_) { $self->{'_currentHSP'}{$name} = $data; } $self->end_element({'Name' => 'Hsp'}); } $self->end_element({'Name' => 'Hit'}); } # adjust result's algorithm name, end output and return $self->element({'Name' => 'Sim4Output_program', 'Data' => $DEFAULTFORMAT . ' (A=' . (defined $format ? $format : '?') . ')'}); $self->end_element({'Name' => 'Sim4Output'}); return $self->end_document(); } return; } =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( $self->_will_handle($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( $nm eq 'Hsp' ) { $self->{'_currentHSP'}{'Hsp_midline'} ||= ''; $self->{'_currentHSP'}{'Hsp_query-to'} ||= $self->{'_currentHSP'}{'Hsp_query-from'} + length($self->{'_currentHSP'}{'Hsp_qseq'}) - 1 - $self->{'_currentHSP'}{'Hsp_querygaps'}; $self->{'_currentHSP'}{'Hsp_hit-to'} ||= $self->{'_currentHSP'}{'Hsp_hit-from'} + length($self->{'_currentHSP'}{'Hsp_hseq'}) - 1 - $self->{'_currentHSP'}{'Hsp_hitgaps'}; $self->{'_currentHSP'}{'Hsp_identity'} ||= ($self->{'_currentHSP'}{'Hsp_midline'} =~ tr/\|//); $self->{'_currentHSP'}{'Hsp_qlength'} ||= abs($self->{'_currentHSP'}{'Hsp_query-to'} - $self->{'_currentHSP'}{'Hsp_query-from'}) + 1; $self->{'_currentHSP'}{'Hsp_hlength'} ||= abs($self->{'_currentHSP'}{'Hsp_hit-to'} - $self->{'_currentHSP'}{'Hsp_hit-from'}) + 1; $self->{'_currentHSP'}{'Hsp_align-len'} ||= abs($self->{'_currentHSP'}{'Hsp_query-to'} - $self->{'_currentHSP'}{'Hsp_query-from'}) + 1; $self->{'_currentHSP'}{'Hsp_score'} ||= int(100 * ($self->{'_currentHSP'}{'Hsp_identity'} / $self->{'_currentHSP'}{'Hsp_align-len'})); foreach (keys %{$self->{'_currentHSP'}}) { $self->element({'Name' => $_, 'Data' => delete ${$self->{'_currentHSP'}}{$_}}); } } if( $type = $MODEMAP{$nm} ) { if( $self->_will_handle($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'} && $data->{'Data'} !~ /^\s+$/ ); if( $self->in_element('hsp') && $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) { $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'}; } $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'} = $DEFAULTFORMAT; } =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 { return 1; # can a sim4 report contain more than one result? } sub report_count { shift->result_count } =head2 _will_handle Title : _will_handle Usage : Private method. For internal use only. if( $self->_will_handle($type) ) { ... } Function: Provides an optimized way to check whether or not an element of a given type is to be handled. Returns : Reference to EventHandler object if the element type is to be handled. undef if the element type is not to be handled. Args : string containing type of element. Optimizations: 1. Using the cached pointer to the EventHandler to minimize repeated lookups. 2. Caching the will_handle status for each type that is encountered so that it only need be checked by calling handler->will_handle($type) once. This does not lead to a major savings by itself (only 5-10%). In combination with other optimizations, or for large parse jobs, the savings good be significant. To test against the unoptimized version, remove the parentheses from around the third term in the ternary " ? : " operator and add two calls to $self-E_eventHandler(). =cut sub _will_handle { my ($self,$type) = @_; my $handler = $self->{'_handler_cache'} ||= $self->_eventHandler; my $will_handle = defined($self->{'_will_handle_cache'}->{$type}) ? $self->{'_will_handle_cache'}->{$type} : ($self->{'_will_handle_cache'}->{$type} = $handler->will_handle($type)); return $will_handle ? $handler : undef; } 1;