# $Id: GenericHSP.pm,v 1.60 2003/12/06 18:12:02 jason Exp $ # # BioPerl module for Bio::Search::HSP::GenericHSP # # 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::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair =head1 SYNOPSIS my $hsp = new Bio::Search::HSP::GenericHSP( -algorithm => 'blastp', -evalue => '1e-30', ); $r_type = $hsp->algorithm; $pvalue = $hsp->p(); $evalue = $hsp->evalue(); $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] ); $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] ); $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); $qseq = $hsp->query_string; $hseq = $hsp->hit_string; $homo_string = $hsp->homology_string; $len = $hsp->length( ['query'|'hit'|'total'] ); $len = $hsp->length( ['query'|'hit'|'total'] ); $rank = $hsp->rank; # TODO: Describe how to configure a SearchIO stream so that it generates # GenericHSP objects. =head1 DESCRIPTION This implementation is "Generic", meaning it is is suitable for holding information about High Scoring pairs from most Search reports such as BLAST and FastA. Specialized objects can be derived from this. Unless you're writing a parser, you won't ever need to create a GenericHSP or any other HSPI-implementing object. If you use the SearchIO system, HSPI objects are created automatically from a SearchIO stream which returns Bio::Search::Result::ResultI objects and you get the HSPI objects via the ResultI API. For documentation on what you can do with GenericHSP (and other HSPI objects), please see the API documentation in L. =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/MailList.shtml - About the mailing lists =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: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Jason Stajich and Steve Chervitz Email jason@bioperl.org Email sac@bioperl.org Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =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::Search::HSP::GenericHSP; use vars qw(@ISA $GAP_SYMBOL); use strict; use Bio::Root::Root; use Bio::SeqFeature::Similarity; use Bio::Search::HSP::HSPI; @ISA = qw(Bio::Search::HSP::HSPI); BEGIN { $GAP_SYMBOL = '-'; } =head2 new Title : new Usage : my $obj = new Bio::Search::HSP::GenericHSP(); Function: Builds a new Bio::Search::HSP::GenericHSP object Returns : Bio::Search::HSP::GenericHSP Args : -algorithm => algorithm used (BLASTP, TBLASTX, FASTX, etc) -evalue => evalue -pvalue => pvalue -bits => bit value for HSP -score => score value for HSP (typically z-score but depends on analysis) -hsp_length=> Length of the HSP (including gaps) -identical => # of residues that that matched identically -percent_identity => (optional) percent identity -conserved => # of residues that matched conservatively (only protein comparisions; conserved == identical in nucleotide comparisons) -hsp_gaps => # of gaps in the HSP -query_gaps => # of gaps in the query in the alignment -hit_gaps => # of gaps in the subject in the alignment -query_name => HSP Query sequence name (if available) -query_start => HSP Query start (in original query sequence coords) -query_end => HSP Query end (in original query sequence coords) -hit_name => HSP Hit sequence name (if available) -hit_start => HSP Hit start (in original hit sequence coords) -hit_end => HSP Hit end (in original hit sequence coords) -hit_length => total length of the hit sequence -query_length=> total length of the query sequence -query_seq => query sequence portion of the HSP -hit_seq => hit sequence portion of the HSP -homology_seq=> homology sequence for the HSP -hit_frame => hit frame (only if hit is translated protein) -query_frame => query frame (only if query is translated protein) -rank => HSP rank -links => HSP links information (WU-BLAST only) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($algo, $evalue, $pvalue, $identical, $percent_id,$conserved, $gaps, $query_gaps, $hit_gaps, $hit_seq, $query_seq, $homology_seq, $hsp_len, $query_len,$hit_len, $hit_name,$query_name,$bits,$score, $hs,$he,$qs,$qe, $qframe,$hframe, $links, $rank) = $self->_rearrange([qw(ALGORITHM EVALUE PVALUE IDENTICAL PERCENT_IDENTITY CONSERVED HSP_GAPS QUERY_GAPS HIT_GAPS HIT_SEQ QUERY_SEQ HOMOLOGY_SEQ HSP_LENGTH QUERY_LENGTH HIT_LENGTH HIT_NAME QUERY_NAME BITS SCORE HIT_START HIT_END QUERY_START QUERY_END QUERY_FRAME HIT_FRAME LINKS RANK )], @args); $algo = 'GENERIC' unless defined $algo; $self->algorithm($algo); # defined $evalue && $self->evalue($evalue) # $hsp->significance is initialized by the # the SimilarityPair object - let's only keep one # value, don't need 2 slots. defined $pvalue && $self->pvalue($pvalue); defined $bits && $self->bits($bits); defined $score && $self->score($score); my ($queryfactor, $hitfactor) = (0,0); if( $algo =~ /^(PSI)?T(BLAST|FAST|SW)[NY]/oi ) { $hitfactor = 1; } elsif ($algo =~ /^(FAST|BLAST)(X|Y|XY)/oi || $algo =~ /^P?GENEWISE/oi ) { $queryfactor = 1; } elsif ($algo =~ /^T(BLAST|FAST|SW)(X|Y|XY)/oi || $algo =~ /^(BLAST|FAST|SW)N/oi || $algo =~ /^WABA|AXT|BLAT|BLASTZ|PSL|MEGABLAST|EXONERATE|SW|SMITH\-WATERMAN|SIM4$/ ){ $hitfactor = 1; $queryfactor = 1; } elsif( $algo eq 'RPSBLAST' ) { $queryfactor = $hitfactor = 0; $qframe = $hframe = 0; } # Store the aligned query as sequence feature my $strand; unless( defined $qe && defined $qs ) { $self->throw("Did not specify a Query End or Query Begin @args (qs='".$qs||''."',qe='?".$qe."')"); } unless( defined $he && defined $hs ) { $self->throw("Did not specify a Hit End or Hit Begin"); } if ($qe > $qs) { # normal query: start < end if ($queryfactor) { $strand = 1; } else { $strand = undef; } } else { # reverse query (i dont know if this is possible, # but feel free to correct) if ($queryfactor) { $strand = -1; } else { $strand = undef; } ($qs,$qe) = ($qe,$qs); } # Note: many of these data are not query- and hit-specific. # Only start, end, name, length are. # We could be more efficient by only storing this info once. # steve chervitz --- Sat Apr 5 00:55:07 2003 $self->query( new Bio::SeqFeature::Similarity ('-primary' => $self->primary_tag, '-start' => $qs, '-expect' => $evalue, '-bits' => $bits, '-score' => $score, '-end' => $qe, '-strand' => $strand, '-seq_id' => $query_name, '-seqlength'=> $query_len, '-source' => $algo, ) ); # to determine frame from something like FASTXY which doesn't # report the frame if( defined $strand && ! defined $qframe && $queryfactor ) { $qframe = ( $self->query->start % 3 ) * $strand; } elsif( ! defined $strand ) { $qframe = 0; } # store the aligned subject as sequence feature if ($he > $hs) { # normal subject if ($hitfactor) { $strand = 1; } else { $strand = undef; } } else { if ($hitfactor) { $strand = -1; } else { $strand = undef; } ($hs,$he) = ( $he,$hs); # reverse subject: start bigger than end } $self->hit( Bio::SeqFeature::Similarity->new ('-start' => $hs, '-end' => $he, '-strand' => $strand, '-expect' => $evalue, '-bits' => $bits, '-score' => $score, '-source' => $algo, '-seq_id' => $hit_name, '-seqlength' => $hit_len, '-primary' => $self->primary_tag )); if( defined $strand && ! defined $hframe && $hitfactor ) { $hframe = ( $hs % 3 ) * $strand; } elsif( ! defined $strand ) { $hframe = 0; } $self->frame($qframe,$hframe); if( ! defined $query_len || ! defined $hit_len ) { $self->throw("Must defined hit and query length"); } if( ! defined $identical ) { if( ! defined $percent_id ) { $self->warn("Did not defined the number of identical matches or overall percent identity in the HSP assuming 0"); $identical = 0; } else { $identical = int($percent_id * $hsp_len); } } if( ! defined $conserved ) { $self->warn("Did not defined the number of conserved matches in the HSP assuming conserved == identical ($identical)") if( $algo !~ /^((FAST|BLAST)N)|EXONERATE|SIM4|AXT|PSL|BLAT|BLASTZ|WABA/oi); $conserved = $identical; } # protect for divide by zero if user does not specify # hsp_len, query_len, or hit_len $self->num_identical($identical); $self->num_conserved($conserved); if( $hsp_len ) { $self->length('total', $hsp_len); $self->frac_identical( 'total', $identical / $self->length('total')); $self->frac_conserved( 'total', $conserved / $self->length('total')); } if( $hit_len ) { # $self->length('hit', $self->hit->length); $self->frac_identical( 'hit', $identical / $self->length('hit')); $self->frac_conserved( 'hit', $conserved / $self->length('hit')); } if( $query_len ) { # $self->length('query', $self->query->length); $self->frac_identical( 'query', $identical / $self->length('query')) ; $self->frac_conserved( 'query', $conserved / $self->length('query')); } $self->query_string($query_seq); $self->hit_string($hit_seq); $self->homology_string($homology_seq); if( defined $query_gaps ) { $self->gaps('query', $query_gaps); } elsif( defined $query_seq ) { $self->gaps('query', scalar ( $query_seq =~ tr/\-//)); } if( defined $hit_gaps ) { $self->gaps('hit', $hit_gaps); } elsif( defined $hit_seq ) { $self->gaps('hit', scalar ( $hit_seq =~ tr/\-//)); } if( ! defined $gaps ) { $gaps = $self->gaps("query") + $self->gaps("hit"); } $self->gaps('total', $gaps); $self->percent_identity($percent_id || $identical / $hsp_len ) if( $hsp_len > 0 ); defined $rank && $self->rank($rank); defined $links && $self->links($links); return $self; } =head2 L methods Implementation of L methods follow =head2 algorithm Title : algorithm Usage : my $r_type = $hsp->algorithm Function: Obtain the name of the algorithm used to obtain the HSP Returns : string (e.g., BLASTP) Args : [optional] scalar string to set value =cut sub algorithm{ my ($self,$value) = @_; my $previous = $self->{'_algorithm'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_algorithm'} = $value; } return $previous; } =head2 pvalue Title : pvalue Usage : my $pvalue = $hsp->pvalue(); Function: Returns the P-value for this HSP or undef Returns : float or exponential (2e-10) P-value is not defined with NCBI Blast2 reports. Args : [optional] numeric to set value =cut sub pvalue { my ($self,$value) = @_; my $previous = $self->{'_pvalue'}; if( defined $value ) { $self->{'_pvalue'} = $value; } return $previous; } =head2 evalue Title : evalue Usage : my $evalue = $hsp->evalue(); Function: Returns the e-value for this HSP Returns : float or exponential (2e-10) Args : [optional] numeric to set value =cut sub evalue { shift->significance(@_) } # Override significance to return the e-value or, if this is # not defined (WU-BLAST), return the p-value. sub significance { my $self = shift; my $signif = $self->query->significance(@_); return (defined $signif && $signif ne '') ? $signif : $self->pvalue(@_); } =head2 frac_identical Title : frac_identical Usage : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] ); Function: Returns the fraction of identitical positions for this HSP Returns : Float in range 0.0 -> 1.0 Args : arg 1: 'query' = num identical / length of query seq (without gaps) 'hit' = num identical / length of hit seq (without gaps) synonyms: 'sbjct', 'subject' 'total' = num conserved / length of alignment (with gaps) synonyms: 'hsp' default = 'total' arg 2: [optional] frac identical value to set for the type requested =cut sub frac_identical { my ($self, $type,$value) = @_; $type = lc $type if defined $type; $type = 'hit' if( defined $type && $type =~ /subject|sbjct/); $type = 'total' if( ! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/); my $previous = $self->{'_frac_identical'}->{$type}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; if( $type eq 'hit' || $type eq 'query' ) { $self->$type()->frac_identical( $value); } $self->{'_frac_identical'}->{$type} = $value; } return $previous; } =head2 frac_conserved Title : frac_conserved Usage : my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] ); Function : Returns the fraction of conserved positions for this HSP. This is the fraction of symbols in the alignment with a positive score. Returns : Float in range 0.0 -> 1.0 Args : arg 1: 'query' = num conserved / length of query seq (without gaps) 'hit' = num conserved / length of hit seq (without gaps) synonyms: 'sbjct', 'subject' 'total' = num conserved / length of alignment (with gaps) synonyms: 'hsp' default = 'total' arg 2: [optional] frac conserved value to set for the type requested =cut sub frac_conserved { my ($self, $type,$value) = @_; $type = lc $type if defined $type; $type = 'hit' if( defined $type && $type =~ /subject|sbjct/); $type = 'total' if( ! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/); my $previous = $self->{'_frac_conserved'}->{$type}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_frac_conserved'}->{$type} = $value; } return $previous; } =head2 gaps Title : gaps Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); Function : Get the number of gaps in the query, hit, or total alignment. Returns : Integer, number of gaps or 0 if none Args : arg 1: 'query' = num gaps in query seq 'hit' = num gaps in hit seq; synonyms: 'sbjct', 'subject' 'total' = num gaps in whole alignment; synonyms: 'hsp' default = 'total' arg 2: [optional] integer gap value to set for the type requested =cut sub gaps { my ($self, $type,$value) = @_; $type = lc $type if defined $type; $type = 'total' if( ! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/); $type = 'hit' if $type =~ /sbjct|subject/; my $previous = $self->{'_gaps'}->{$type}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_gaps'}->{$type} = $value; } return $previous || 0; } =head2 query_string Title : query_string Usage : my $qseq = $hsp->query_string; Function: Retrieves the query sequence of this HSP as a string Returns : string Args : [optional] string to set for query sequence =cut sub query_string{ my ($self,$value) = @_; my $previous = $self->{'_query_string'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_query_string'} = $value; # do some housekeeping so we know when to # re-run _calculate_seq_positions $self->{'_sequenceschanged'} = 1; } return $previous; } =head2 hit_string Title : hit_string Usage : my $hseq = $hsp->hit_string; Function: Retrieves the hit sequence of this HSP as a string Returns : string Args : [optional] string to set for hit sequence =cut sub hit_string{ my ($self,$value) = @_; my $previous = $self->{'_hit_string'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_hit_string'} = $value; # do some housekeeping so we know when to # re-run _calculate_seq_positions $self->{'_sequenceschanged'} = 1; } return $previous; } =head2 homology_string Title : homology_string Usage : my $homo_string = $hsp->homology_string; Function: Retrieves the homology sequence for this HSP as a string. : The homology sequence is the string of symbols in between the : query and hit sequences in the alignment indicating the degree : of conservation (e.g., identical, similar, not similar). Returns : string Args : [optional] string to set for homology sequence =cut sub homology_string{ my ($self,$value) = @_; my $previous = $self->{'_homology_string'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_homology_string'} = $value; # do some housekeeping so we know when to # re-run _calculate_seq_positions $self->{'_sequenceschanged'} = 1; } return $previous; } =head2 length Title : length Usage : my $len = $hsp->length( ['query'|'hit'|'total'] ); Function : Returns the length of the query or hit in the alignment (without gaps) or the aggregate length of the HSP (including gaps; this may be greater than either hit or query ) Returns : integer Args : arg 1: 'query' = length of query seq (without gaps) 'hit' = length of hit seq (without gaps) (synonyms: sbjct, subject) 'total' = length of alignment (with gaps) default = 'total' arg 2: [optional] integer length value to set for specific type =cut sub length { my $self = shift; my $type = shift; $type = 'total' unless defined $type; $type = lc $type; if( $type =~ /^q/i ) { return $self->query()->length(shift); } elsif( $type =~ /^(hit|subject|sbjct)/ ) { return $self->hit()->length(shift); } else { my $v = shift; if( defined $v ) { $self->{'_hsplength'} = $v; } return $self->{'_hsplength'}; } return 0; # should never get here } =head2 hsp_length Title : hsp_length Usage : my $len = $hsp->hsp_length() Function: shortcut length('hsp') Returns : floating point between 0 and 100 Args : none =cut sub hsp_length { return shift->length('hsp', shift); } =head2 percent_identity Title : percent_identity Usage : my $percentid = $hsp->percent_identity() Function: Returns the calculated percent identity for an HSP Returns : floating point between 0 and 100 Args : none =cut =head2 frame Title : frame Usage : $hsp->frame($queryframe,$subjectframe) Function: Set the Frame for both query and subject and insure that they agree. This overrides the frame() method implementation in FeaturePair. Returns : array of query and subjects if return type wants an array or query frame if defined or subject frame Args : none Note : Frames are stored in the GFF way (0-2) not 1-3 as they are in BLAST (negative frames are deduced by checking the strand of the query or hit) =cut sub frame { my ($self, $qframe, $sframe) = @_; if( defined $qframe ) { if( $qframe == 0 ) { $qframe = 0; } elsif( $qframe !~ /^([+-])?([1-3])/ ) { $self->warn("Specifying an invalid query frame ($qframe)"); $qframe = undef; } else { my $dir = $1; $dir = '+' unless defined $dir; if( ($dir eq '-' && $self->query->strand >= 0) || ($dir eq '+' && $self->query->strand <= 0) ) { $self->warn("Query frame ($qframe) did not match strand of query (". $self->query->strand() . ")"); } # Set frame to GFF [0-2] - # what if someone tries to put in a GFF frame! $qframe = $2 - 1; } $self->query->frame($qframe); } if( defined $sframe ) { if( $sframe == 0 ) { $sframe = 0; } elsif( $sframe !~ /^([+-])?([1-3])/ ) { $self->warn("Specifying an invalid subject frame ($sframe)"); $sframe = undef; } else { my $dir = $1; $dir = '+' unless defined $dir; if( ($dir eq '-' && $self->hit->strand >= 0) || ($dir eq '+' && $self->hit->strand <= 0) ) { $self->warn("Subject frame ($sframe) did not match strand of subject (". $self->hit->strand() . ")"); } # Set frame to GFF [0-2] $sframe = $2 - 1; } $self->hit->frame($sframe); } if (wantarray() && $self->algorithm =~ /^T(BLAST|FAST)(X|Y|XY)/oi) { return ($self->query->frame(), $self->hit->frame()); } elsif (wantarray()) { ($self->query->frame() && return ($self->query->frame(), undef)) || ($self->hit->frame() && return (undef, $self->hit->frame())); } else { ($self->query->frame() && return $self->query->frame()) || ($self->hit->frame() && return $self->hit->frame()); } } =head2 get_aln Title : get_aln Usage : my $aln = $hsp->gel_aln Function: Returns a L object representing the HSP alignment Returns : L Args : none =cut sub get_aln { my ($self) = @_; require Bio::LocatableSeq; require Bio::SimpleAlign; my $aln = new Bio::SimpleAlign; my $hs = $self->hit_string(); my $qs = $self->query_string(); # FASTA specific stuff moved to the FastaHSP object my $seqonly = $qs; $seqonly =~ s/[\-\s]//g; my ($q_nm,$s_nm) = ($self->query->seq_id(), $self->hit->seq_id()); unless( defined $q_nm && CORE::length ($q_nm) ) { $q_nm = 'query'; } unless( defined $s_nm && CORE::length ($s_nm) ) { $s_nm = 'hit'; } my $query = new Bio::LocatableSeq('-seq' => $qs, '-id' => $q_nm, '-start' => $self->query->start, '-end' => $self->query->end, ); $seqonly = $hs; $seqonly =~ s/[\-\s]//g; my $hit = new Bio::LocatableSeq('-seq' => $hs, '-id' => $s_nm, '-start' => $self->hit->start, '-end' => $self->hit->end, ); $aln->add_seq($query); $aln->add_seq($hit); return $aln; } =head2 num_conserved Title : num_conserved Usage : $obj->num_conserved($newval) Function: returns the number of conserved residues in the alignment Returns : inetger Args : integer (optional) =cut sub num_conserved{ my ($self,$value) = @_; if( defined $value) { $self->{'num_conserved'} = $value; } return $self->{'num_conserved'}; } =head2 num_identical Title : num_identical Usage : $obj->num_identical($newval) Function: returns the number of identical residues in the alignment Returns : integer Args : integer (optional) =cut sub num_identical{ my ($self,$value) = @_; if( defined $value) { $self->{'_num_identical'} = $value; } return $self->{'_num_identical'}; } =head2 rank Usage : $hsp->rank( [string] ); Purpose : Get the rank of the HSP within a given Blast hit. Example : $rank = $hsp->rank; Returns : Integer (1..n) corresponding to the order in which the HSP appears in the BLAST report. =cut sub rank { my ($self,$value) = @_; if( defined $value) { $self->{'_rank'} = $value; } return $self->{'_rank'}; } =head2 seq_inds Title : seq_inds Purpose : Get a list of residue positions (indices) for all identical : or conserved residues in the query or sbjct sequence. Example : @s_ind = $hsp->seq_inds('query', 'identical'); : @h_ind = $hsp->seq_inds('hit', 'conserved'); @h_ind = $hsp->seq_inds('hit', 'conserved-not-identical'); : @h_ind = $hsp->seq_inds('hit', 'conserved', 1); Returns : List of integers : May include ranges if collapse is true. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query) : ('sbjct' is synonymous with 'hit') : class = 'identical' or 'conserved' or 'nomatch' or 'gap' : (default = identical) : (can be shortened to 'id' or 'cons') : or 'conserved-not-identical' : collapse = boolean, if true, consecutive positions are merged : using a range notation, e.g., "1 2 3 4 5 7 9 10 11" : collapses to "1-5 7 9-11". This is useful for : consolidating long lists. Default = no collapse. Throws : n/a. Comments : See Also : L, L =cut sub seq_inds{ my ($self, $seqType, $class, $collapse) = @_; # prepare the internal structures - this is cached so # if the strings have not changed we're okay $self->_calculate_seq_positions(); $seqType ||= 'query'; $class ||= 'identical'; $collapse ||= 0; $seqType = 'sbjct' if $seqType eq 'hit'; my $t = lc(substr($seqType,0,1)); if( $t eq 'q' ) { $seqType = 'query'; } elsif ( $t eq 's' || $t eq 'h' ) { $seqType = 'sbjct'; } else { $self->warn("unknown seqtype $seqType using 'query'"); $seqType = 'query'; } $t = lc(substr($class,0,1)); if( $t eq 'c' ) { if( $class =~ /conserved\-not\-identical/ ) { $class = 'conserved'; } else { $class = 'conservedall'; } } elsif( $t eq 'i' ) { $class = 'identical'; } elsif( $t eq 'n' ) { $class = 'nomatch'; } elsif( $t eq 'g' ) { $class = 'gap'; } else { $self->warn("unknown sequence class $class using 'identical'"); $class = 'identical'; } ## Sensitive to member name changes. $seqType = "_\L$seqType\E"; $class = "_\L$class\E"; my @ary; if( $class eq '_gap' ) { # this means that we are remapping the gap length that is stored # in the hash (for example $self->{'_gapRes_query'} ) # so we'll return an array which has the values of the position of the # of the gap (the key in the hash) + the gap length (value in the # hash for this key - 1. @ary = map { $_ > 1 ? $_..($_ + $self->{"${class}Res$seqType"}->{$_} - 1) : $_ } sort { $a <=> $b } keys %{ $self->{"${class}Res$seqType"}}; } elsif( $class eq '_conservedall' ) { @ary = sort { $a <=> $b } keys %{ $self->{"_conservedRes$seqType"}}, keys %{ $self->{"_identicalRes$seqType"}}, } else { @ary = sort { $a <=> $b } keys %{ $self->{"${class}Res$seqType"}}; } require Bio::Search::BlastUtils if $collapse; return $collapse ? &Bio::Search::SearchUtils::collapse_nums(@ary) : @ary; } =head2 Inherited from L These methods come from L =head2 query Title : query Usage : my $query = $hsp->query Function: Returns a SeqFeature representing the query in the HSP Returns : L Args : [optional] new value to set =head2 hit Title : hit Usage : my $hit = $hsp->hit Function: Returns a SeqFeature representing the hit in the HSP Returns : L Args : [optional] new value to set =head2 significance Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Get/Set the significance value Returns : numeric Args : [optional] new value to set =head2 bits Title : bits Usage : $bits = $obj->bits(); $obj->bits($value); Function: Get/Set the bits value Returns : numeric Args : [optional] new value to set =head2 strand Title : strand Usage : $hsp->strand('query') Function: Retrieves the strand for the HSP component requested Returns : +1 or -1 (0 if unknown) Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject 'query' to retrieve the query strand (default) =cut =head1 Private methods =cut =head2 _calculate_seq_positions Title : _calculate_seq_positions Usage : $self->_calculate_seq_positions Function: Internal function Returns : Args : =cut sub _calculate_seq_positions { my ($self,@args) = @_; return unless ( $self->{'_sequenceschanged'} ); $self->{'_sequenceschanged'} = 0; my ($mchar, $schar, $qchar); my ($seqString, $qseq,$sseq) = ( $self->homology_string(), $self->query_string(), $self->hit_string() ); # Using hashes to avoid saving duplicate residue numbers. my %identicalList_query = (); my %identicalList_sbjct = (); my %conservedList_query = (); my %conservedList_sbjct = (); my %gapList_query = (); my %gapList_sbjct = (); my %nomatchList_query = (); my %nomatchList_sbjct = (); my $qdir = $self->query->strand || 1; my $sdir = $self->hit->strand || 1; my $resCount_query = ($qdir >=0) ? $self->query->end : $self->query->start; my $resCount_sbjct = ($sdir >=0) ? $self->hit->end : $self->hit->start; my $prog = $self->algorithm; if( $prog =~ /FAST/i ) { # fasta reports some extra 'regional' sequence information # we need to clear out first # this seemed a bit insane to me at first, but it appears to # work --jason # we infer the end of the regional sequence where the first # non space is in the homology string # then we use the HSP->length to tell us how far to read # to cut off the end of the sequence # one possible problem is the sequence which my ($start) = (0); if( $seqString =~ /^(\s+)/ ) { $start = CORE::length($1); } $seqString = substr($seqString, $start,$self->length('total')); $qseq = substr($qseq, $start,$self->length('total')); $sseq = substr($sseq, $start,$self->length('total')); $qseq =~ s![\\\/]!!g; $sseq =~ s![\\\/]!!g; } if($prog =~ /^(PSI)?T(BLAST|FAST)N/oi ) { $resCount_sbjct = int($resCount_sbjct / 3); } elsif($prog =~ /^(BLAST|FAST)(X|Y|XY)/oi ) { $resCount_query = int($resCount_query / 3); } elsif($prog =~ /^T(BLAST|FAST)(X|Y|XY)/oi ) { $resCount_query = int($resCount_query / 3); $resCount_sbjct = int($resCount_sbjct / 3); } while( $mchar = chop($seqString) ) { ($qchar, $schar) = (chop($qseq), chop($sseq)); if( $mchar eq '+' || $mchar eq '.' || $mchar eq ':' ) { $conservedList_query{ $resCount_query } = 1; $conservedList_sbjct{ $resCount_sbjct } = 1; } elsif( $mchar ne ' ' ) { $identicalList_query{ $resCount_query } = 1; $identicalList_sbjct{ $resCount_sbjct } = 1; } elsif( $mchar eq ' ') { $nomatchList_query{ $resCount_query } = 1; $nomatchList_sbjct{ $resCount_sbjct } = 1; } if( $qchar eq $GAP_SYMBOL ) { $gapList_query{ $resCount_query } ++; } else { $resCount_query -= $qdir; } if( $schar eq $GAP_SYMBOL ) { $gapList_sbjct{ $resCount_query } ++; } else { $resCount_sbjct -=$sdir; } } $self->{'_identicalRes_query'} = \%identicalList_query; $self->{'_conservedRes_query'} = \%conservedList_query; $self->{'_nomatchRes_query'} = \%nomatchList_query; $self->{'_gapRes_query'} = \%gapList_query; $self->{'_identicalRes_sbjct'} = \%identicalList_sbjct; $self->{'_conservedRes_sbjct'} = \%conservedList_sbjct; $self->{'_nomatchRes_sbjct'} = \%nomatchList_sbjct; $self->{'_gapRes_sbjct'} = \%gapList_sbjct; return 1; } =head2 n See documentation in L =cut #----- sub n { my $self = shift; if(@_) { $self->{'_n'} = shift; } defined $self->{'_n'} ? $self->{'_n'} : ''; } =head2 range See documentation in L =cut #---------- sub range { #---------- my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; my ($start, $end); if( $seqType eq 'query' ) { $start = $self->query->start; $end = $self->query->end; } else { $start = $self->hit->start; $end = $self->hit->end; } return ($start, $end); } =head2 links Title : links Usage : $obj->links($newval) Function: Get/Set the Links value (from WU-BLAST) Indicates the placement of the alignment in the group of HSPs Returns : Value of links Args : On set, new value (a scalar or undef, optional) =cut sub links{ my $self = shift; return $self->{'links'} = shift if @_; return $self->{'links'}; } # The cigar string code is written by Juguang Xiao =head1 Brief introduction on cigar string NOTE: the concept is originally from EnsEMBL docs at http://www.ensembl.org/Docs/wiki/html/EnsemblDocs/CigarFormat.html. Please append to these docs if you have a better definition. Sequence alignment hits can be stored in a database as ungapped alignments. This imposes 2 major constraints on alignments: a) alignments for a single hit record require multiple rows in the database, and b) it is not possible to accurately retrieve the exact original alignment. Alternatively, sequence alignments can be stored as gapped alignments using the CIGAR line format (where CIGAR stands for Concise Idiosyncratic Gapped Alignment Report). In the cigar line format alignments are stored as follows: M: Match D: Deletion I: Insertion An example of an alignment for a hypthetical protein match is shown below: Query: 42 PGPAGLP----GSVGLQGPRGLRGPLP-GPLGPPL... PG P G GP R PLGP Sbjct: 1672 PGTP*TPLVPLGPWVPLGPSSPR--LPSGPLGPTD... protein_align_feature table as the following cigar line: 7M4D12M2I2MD7M =head2 cigar_string Name: cigar_string Usage: $cigar_string = $hsp->cigar_string Function: Generate and return cigar string for this HSP alignment Args: No input needed Return: a cigar string =cut sub cigar_string { my ($self, $arg) = @_; $self->warn("this is not a setter") if(defined $arg); unless(defined $self->{_cigar_string}){ # generate cigar string my $cigar_string = $self->generate_cigar_string($self->query_string, $self->hit_string); $self->{_cigar_string} = $cigar_string; } # end of unless return $self->{_cigar_string}; } =head2 generate_cigar_string Name: generate_cigar_string Usage: my $cigar_string = Bio::Search::HSP::GenericHSP::generate_cigar_string ($qstr, $hstr); Function: generate cigar string from a simple sequence of alignment. Args: the string of query and subject Return: cigar string =cut sub generate_cigar_string { my ($self, $qstr, $hstr) = @_; my @qchars = split //, $qstr; my @hchars = split //, $hstr; unless(scalar(@qchars) == scalar(@hchars)){ $self->throw("two sequences are not equal in lengths"); } $self->{_count_for_cigar_string} = 0; $self->{_state_for_cigar_string} = 'M'; my $cigar_string = ''; for(my $i=0; $i <= $#qchars; $i++){ my $qchar = $qchars[$i]; my $hchar = $hchars[$i]; if($qchar ne $GAP_SYMBOL && $hchar ne $GAP_SYMBOL){ # Match $cigar_string .= $self->_sub_cigar_string('M'); }elsif($qchar eq $GAP_SYMBOL){ # Deletion $cigar_string .= $self->_sub_cigar_string('D'); }elsif($hchar eq $GAP_SYMBOL){ # Insertion $cigar_string .= $self->_sub_cigar_string('I'); }else{ $self->throw("Impossible state that 2 gaps on each seq aligned"); } } $cigar_string .= $self->_sub_cigar_string('X'); # not forget the tail. return $cigar_string; } # an internal method to help generate cigar string sub _sub_cigar_string { my ($self, $new_state) = @_; my $sub_cigar_string = ''; if($self->{_state_for_cigar_string} eq $new_state){ $self->{_count_for_cigar_string} += 1; # Remain the state and increase the counter }else{ $sub_cigar_string .= $self->{_count_for_cigar_string} unless $self->{_count_for_cigar_string} == 1; $sub_cigar_string .= $self->{_state_for_cigar_string}; $self->{_count_for_cigar_string} = 1; $self->{_state_for_cigar_string} = $new_state; } return $sub_cigar_string; } 1;