Raw content of Bio::Search::HSP::HSPI #----------------------------------------------------------------- # $Id: HSPI.pm,v 1.21.2.1 2003/01/22 22:51:00 jason Exp $ # # BioPerl module for Bio::Search::HSP::HSPI # # Cared for by Steve Chervitz <sac@bioperl.org> # and Jason Stajich <jason@bioperl.org> # # You may distribute this module under the same terms as perl itself #----------------------------------------------------------------- # POD documentation - main docs before the code =head1 NAME Bio::Search::HSP::HSPI - Interface for a High Scoring Pair in a similarity search result =head1 SYNOPSIS $r_type = $hsp->algorithm $pvalue = $hsp->pvalue(); $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; $homology_string = $hsp->homology_string; $len = $hsp->length( ['query'|'hit'|'total'] ); $rank = $hsp->rank; =head1 DESCRIPTION Bio::Search::HSP::HSPI objects cannot be instantiated since this module defines a pure interface. Given an object that implements the Bio::Search::HSP::HSPI interface, you can do the following things with it: =head1 SEE ALSO This interface inherits methods from these other modules: L<Bio::SeqFeatureI>, L<Bio::SeqFeature::FeaturePair> L<Bio::SeqFeature::SimilarityPair> Please refer to these modules for documentation of the many additional inherited methods. =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 - Steve Chervitz, Jason Stajich Email sac@bioperl.org Email jason@bioperl.org =head1 COPYRIGHT Copyright (c) 2001 Steve Chervitz, Jason Stajich. All Rights Reserved. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =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::HSPI; use vars qw(@ISA); use Bio::Root::RootI; use Bio::SeqFeature::SimilarityPair; use strict; use Carp; @ISA = qw(Bio::SeqFeature::SimilarityPair Bio::Root::RootI); =head2 algorithm Title : algorithm Usage : my $r_type = $hsp->algorithm Function: Obtain the name of the algorithm used to obtain the HSP Returns : string (e.g., BLASTP) Args : none =cut sub algorithm{ my ($self,@args) = @_; $self->throw_not_implemented; } =head2 pvalue Title : pvalue Usage : my $pvalue = $hsp->pvalue(); Function: Returns the P-value for this HSP or undef Returns : float or exponential (2e-10) P-value is not defined with NCBI Blast2 reports. Args : none =cut sub pvalue { my ($self) = @_; $self->throw_not_implemented; } =head2 evalue Title : evalue Usage : my $evalue = $hsp->evalue(); Function: Returns the e-value for this HSP Returns : float or exponential (2e-10) Args : none =cut sub evalue { my ($self) = @_; $self->throw_not_implemented; } =head2 frac_identical Title : frac_identical Usage : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] ); Function: Returns the fraction of identitical positions for this HSP Returns : Float in range 0.0 -> 1.0 Args : 'query' = num identical / length of query seq (without gaps) 'hit' = num identical / length of hit seq (without gaps) 'total' = num identical / length of alignment (with gaps) default = 'total' =cut sub frac_identical { my ($self, $type) = @_; $self->throw_not_implemented; } =head2 frac_conserved Title : frac_conserved Usage : my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] ); Function : Returns the fraction of conserved positions for this HSP. This is the fraction of symbols in the alignment with a positive score. Returns : Float in range 0.0 -> 1.0 Args : 'query' = num conserved / length of query seq (without gaps) 'hit' = num conserved / length of hit seq (without gaps) 'total' = num conserved / length of alignment (with gaps) default = 'total' =cut sub frac_conserved { my ($self, $type) = @_; $self->throw_not_implemented; } =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{ shift->throw_not_implemented; } =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{ shift->throw_not_implemented(); } =head2 gaps Title : gaps Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); Function : Get the number of gaps in the query, hit, or total alignment. Returns : Integer, number of gaps or 0 if none Args : 'query' = num conserved / length of query seq (without gaps) 'hit' = num conserved / length of hit seq (without gaps) 'total' = num conserved / length of alignment (with gaps) default = 'total' =cut sub gaps { my ($self, $type) = @_; $self->throw_not_implemented; } =head2 query_string Title : query_string Usage : my $qseq = $hsp->query_string; Function: Retrieves the query sequence of this HSP as a string Returns : string Args : none =cut sub query_string{ my ($self) = @_; $self->throw_not_implemented; } =head2 hit_string Title : hit_string Usage : my $hseq = $hsp->hit_string; Function: Retrieves the hit sequence of this HSP as a string Returns : string Args : none =cut sub hit_string{ my ($self) = @_; $self->throw_not_implemented; } =head2 homology_string Title : homology_string Usage : my $homo_string = $hsp->homology_string; Function: Retrieves the homology sequence for this HSP as a string. : The homology sequence is the string of symbols in between the : query and hit sequences in the alignment indicating the degree : of conservation (e.g., identical, similar, not similar). Returns : string Args : none =cut sub homology_string{ my ($self) = @_; $self->throw_not_implemented; } =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 : 'query' = length of query seq (without gaps) 'hit' = length of hit seq (without gaps) 'total' = length of alignment (with gaps) default = 'total' Args : none =cut sub length{ shift->throw_not_implemented(); } =head2 percent_identity Title : percent_identity Usage : my $percentid = $hsp->percent_identity() Function: Returns the calculated percent identity for an HSP Returns : floating point between 0 and 100 Args : none =cut sub percent_identity{ my ($self) = @_; return $self->frac_identical('hsp') * 100; } =head2 get_aln Title : get_aln Usage : my $aln = $hsp->gel_aln Function: Returns a Bio::SimpleAlign representing the HSP alignment Returns : Bio::SimpleAlign Args : none =cut sub get_aln { my ($self) = @_; $self->throw_not_implemented; } =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', 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') 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<Bio::Search::BlastUtils::collapse_nums()|Bio::Search::BlastUtils>, L<Bio::Search::Hit::HitI::seq_inds()|Bio::Search::Hit::HitI> =cut sub seq_inds { shift->throw_not_implemented(); } =head2 Inherited from Bio::SeqFeature::SimilarityPair These methods come from Bio::SeqFeature::SimilarityPair =head2 query Title : query Usage : my $query = $hsp->query Function: Returns a SeqFeature representing the query in the HSP Returns : Bio::SeqFeature::Similarity 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 : Bio::SeqFeature::Similarity Args : [optional] new value to set =head2 significance Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Get/Set the significance value (see Bio::SeqFeature::SimilarityPair) Returns : significance value (scientific notation string) Args : significance value (sci notation string) =head2 score Title : score Usage : my $score = $hsp->score(); Function: Returns the score for this HSP or undef Returns : numeric Args : [optional] numeric to set value =head2 bits Title : bits Usage : my $bits = $hsp->bits(); Function: Returns the bit value for this HSP or undef Returns : numeric Args : none =cut # override =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) 'list' or 'array' to retreive both query and hit together =cut sub strand { my $self = shift; my $val = shift; $val = 'query' unless defined $val; $val =~ s/^\s+//; if( $val =~ /^q/i ) { return $self->query->strand(shift); } elsif( $val =~ /^(hi|s)/i ) { return $self->hit->strand(shift); } elsif ( $val =~ m/^(list|array)/) { return ($self->query->strand(shift), $self->hit->strand(shift)); } else { $self->warn("unrecognized component $val requested\n"); } return 0; } =head2 start Title : start Usage : $hsp->start('query') Function: Retrieves the start for the HSP component requested Returns : integer Args : 'hit' or 'subject' or 'sbjct' to retrieve the start of the subject 'query' to retrieve the query start (default) =cut sub start { my $self = shift; my $val = shift; $val = 'query' unless defined $val; $val =~ s/^\s+//; if( $val =~ /^q/i ) { return $self->query->start(shift); } elsif( $val =~ /^(hi|s)/i ) { return $self->hit->start(shift); } else { $self->warn("unrecognized component $val requested\n"); } return 0; } =head2 end Title : end Usage : $hsp->end('query') Function: Retrieves the end for the HSP component requested Returns : integer Args : 'hit' or 'subject' or 'sbjct' to retrieve the end of the subject 'query' to retrieve the query end (default) =cut sub end { my $self = shift; my $val = shift; $val = 'query' unless defined $val; $val =~ s/^\s+//; if( $val =~ /^q/i ) { return $self->query->end(shift); } elsif( $val =~ /^(hi|s)/i ) { return $self->hit->end(shift); } else { $self->warn("unrecognized component $val requested\n"); } return 0; } =head2 seq_str Usage : $hsp->seq_str( seq_type ); Purpose : Get the full query, sbjct, or 'match' sequence as a string. : The 'match' sequence is the string of symbols in between the : query and sbjct sequences. Example : $str = $hsp->seq_str('query'); Returns : String Argument : seq_Type = 'query' or 'hit' or 'sbjct' or 'match' : ('sbjct' is synonymous with 'hit') : default is 'query' Throws : Exception if the argument does not match an accepted seq_type. Comments : See Also : L<seq()|seq>, L<seq_inds()|seq_inds>, B<_set_match_seq()> =cut sub seq_str { my $self = shift; my $type = shift; if( $type =~ /^q/i ) { return $self->query_string(shift) } elsif( $type =~ /^(s|hi)/i ) { return $self->hit_string(shift)} elsif ( $type =~ /^(ho|ma)/i ) { return $self->hit_string(shift) } else { $self->warn("unknown sequence type $type"); } return ''; } =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 { shift->throw_not_implemented } =head2 matches Usage : $hsp->matches([seq_type], [start], [stop]); Purpose : Get the total number of identical and conservative matches : in the query or sbjct sequence for the given HSP. Optionally can : report data within a defined interval along the seq. : (Note: 'conservative' matches are called 'positives' in the : Blast report.) Example : ($id,$cons) = $hsp_object->matches('hit'); : ($id,$cons) = $hsp_object->matches('query',300,400); Returns : 2-element array of integers Argument : (1) seq_type = 'query' or 'hit' or 'sbjct' (default = query) : ('sbjct' is synonymous with 'hit') : (2) start = Starting coordinate (optional) : (3) stop = Ending coordinate (optional) Throws : Exception if the supplied coordinates are out of range. Comments : Relies on seq_str('match') to get the string of alignment symbols : between the query and sbjct lines which are used for determining : the number of identical and conservative matches. See Also : L<length()|length>, L<gaps()|gaps>, L<seq_str()|seq_str>, L<Bio::Search::Hit::BlastHit::_adjust_contigs()|Bio::Search::Hit::BlastHit> =cut #----------- sub matches { #----------- my( $self, %param ) = @_; my(@data); my($seqType, $beg, $end) = ($param{-SEQ}, $param{-START}, $param{-STOP}); $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; if(!defined $beg && !defined $end) { ## Get data for the whole alignment. push @data, ($self->num_identical, $self->num_conserved); } else { ## Get the substring representing the desired sub-section of aln. $beg ||= 0; $end ||= 0; my($start,$stop) = $self->range($seqType); if($beg == 0) { $beg = $start; $end = $beg+$end; } elsif($end == 0) { $end = $stop; $beg = $end-$beg; } if($end >= $stop) { $end = $stop; } ##ML changed from if (end >stop) else { $end += 1;} ##ML moved from commented position below, makes ##more sense here # if($end > $stop) { $end = $stop; } if($beg < $start) { $beg = $start; } # else { $end += 1;} # my $seq = substr($self->seq_str('match'), $beg-$start, ($end-$beg)); ## ML: START fix for substr out of range error ------------------ my $seq = ""; if (($self->algorithm eq 'TBLASTN') and ($seqType eq 'sbjct')) { $seq = substr($self->seq_str('match'), int(($beg-$start)/3), int(($end-$beg+1)/3)); } elsif (($self->algorithm eq 'BLASTX') and ($seqType eq 'query')) { $seq = substr($self->seq_str('match'), int(($beg-$start)/3), int(($end-$beg+1)/3)); } else { $seq = substr($self->seq_str('match'), $beg-$start, ($end-$beg)); } ## ML: End of fix for substr out of range error ----------------- ## ML: debugging code ## This is where we get our exception. Try printing out the values going ## into this: ## # print STDERR # qq(*------------MY EXCEPTION --------------------\nSeq: ") , # $self->seq_str("$seqType"), qq("\n),$self->rank,",( index:"; # print STDERR $beg-$start, ", len: ", $end-$beg," ), (HSPRealLen:", # CORE::length $self->seq_str("$seqType"); # print STDERR ", HSPCalcLen: ", $stop - $start +1 ," ), # ( beg: $beg, end: $end ), ( start: $start, stop: stop )\n"; ## ML: END DEBUGGING CODE---------- if(!CORE::length $seq) { $self->throw("Undefined sub-sequence ($beg,$end). Valid range = $start - $stop"); } ## Get data for a substring. # printf "Collecting HSP subsection data: beg,end = %d,%d; start,stop = %d,%d\n%s<---\n", $beg, $end, $start, $stop, $seq; # printf "Original match seq:\n%s\n",$self->seq_str('match'); $seq =~ s/ //g; # remove space (no info). my $len_cons = CORE::length $seq; $seq =~ s/\+//g; # remove '+' characters (conservative substitutions) my $len_id = CORE::length $seq; push @data, ($len_id, $len_cons); # printf " HSP = %s\n id = %d; cons = %d\n", $self->rank, $len_id, $len_cons; <STDIN>; } @data; } =head2 n Usage : $hsp_obj->n() Purpose : Get the N value (num HSPs on which P/Expect is based). : This value is not defined with NCBI Blast2 with gapping. Returns : Integer or null string if not defined. Argument : n/a Throws : n/a Comments : The 'N' value is listed in parenthesis with P/Expect value: : e.g., P(3) = 1.2e-30 ---> (N = 3). : Not defined in NCBI Blast2 with gaps. : This typically is equal to the number of HSPs but not always. : To obtain the number of HSPs, use Bio::Search::Hit::HitI::num_hsps(). See Also : L<Bio::SeqFeature::SimilarityPair::score()|Bio::SeqFeature::SimilarityPair> =cut sub n { shift->throw_not_implemented } =head2 range Usage : $hsp->range( [seq_type] ); Purpose : Gets the (start, end) coordinates for the query or sbjct sequence : in the HSP alignment. Example : ($query_beg, $query_end) = $hsp->range('query'); : ($hit_beg, $hit_end) = $hsp->range('hit'); Returns : Two-element array of integers Argument : seq_type = string, 'query' or 'hit' or 'sbjct' (default = 'query') : ('sbjct' is synonymous with 'hit') Throws : n/a Comments : This is a convenience method for constructions such as ($hsp->query->start, $hsp->query->end) =cut sub range { shift->throw_not_implemented } 1;