# $Id: ModelHit.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::Search::Hit::ModelHit # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Hit::ModelHit - A model-based implementation of the Bio::Search::Hit::HitI interface =head1 SYNOPSIS use Bio::Search::Hit::ModelHit; my $hit = Bio::Search::Hit::ModelHit->new(-algorithm => 'rnamotif'); # typically one gets HitI objects from a SearchIO stream via a ResultI use Bio::SearchIO; my $parser = Bio::SearchIO->new(-format => 'infernal', -file => 'trap.inf'); my $result = $parser->next_result; my $hit = $result->next_hit; =head1 DESCRIPTION This object handles the hit data from a database search using models or descriptors instead of sequences, such as Infernal, HMMER, RNAMotif, etc. Unless you're writing a parser, you won't ever need to create a ModelHit or any other HitI-implementing object. If you use the SearchIO system, HitI objects are created automatically from a SearchIO stream which returns Bio::Search::Hit::HitI objects. Note that several HitI-based methods have been overridden from ModelHit due to their unreliability when dealing with queries that aren't sequence-based. It may be possible to reimplement these at a later point, but for the time being they will throw warnings and return w/o results. For documentation on what you can do with ModelHit (and other HitI 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/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 - Chris Fields Email cjfields at bioperl dot org =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::Hit::ModelHit; use strict; use base qw(Bio::Search::Hit::GenericHit); =head1 HitI methods implemented in parent class Bio::Search::Hit::ModelHit =head2 new Title : new Usage : my $obj = Bio::Search::Hit::ModelHit->new(); Function: Builds a new Bio::Search::Hit::ModelHit object Returns : Bio::Search::Hit::ModelHit Args : -name => Name of Hit (required) -description => Description (optional) -accession => Accession number (optional) -ncbi_gi => NCBI GI UID (optional) -length => Length of the Hit (optional) -score => Raw Score for the Hit (optional) -bits => Bit Score for the Hit (optional) -significance => Significance value for the Hit (optional) -algorithm => Algorithm used (BLASTP, FASTX, etc...) -hsps => Array ref of HSPs for this Hit. -found_again => boolean, true if hit appears in a "previously found" section of a PSI-Blast report. -hsp_factory => Bio::Factory::ObjectFactoryI able to create HSPI objects. =cut =head2 add_hsp Title : add_hsp Usage : $hit->add_hsp($hsp) Function: Add a HSP to the collection of HSPs for a Hit Returns : number of HSPs in the Hit Args : Bio::Search::HSP::HSPI object, OR hash ref containing data suitable for creating a HSPI object (&hsp_factory must be set to get it back) =cut =head2 hsp_factory Title : hsp_factory Usage : $hit->hsp_factory($hsp_factory) Function: Get/set the factory used to build HSPI objects if necessary. Returns : Bio::Factory::ObjectFactoryI Args : Bio::Factory::ObjectFactoryI =cut =head2 Bio::Search::Hit::HitI methods Implementation of Bio::Search::Hit::HitI methods =head2 name Title : name Usage : $hit_name = $hit->name(); Function: returns the name of the Hit sequence Returns : a scalar string Args : [optional] scalar string to set the name =cut =head2 accession Title : accession Usage : $acc = $hit->accession(); Function: Retrieve the accession (if available) for the hit Returns : a scalar string (empty string if not set) Args : none =cut =head2 description Title : description Usage : $desc = $hit->description(); Function: Retrieve the description for the hit Returns : a scalar string Args : [optional] scalar string to set the descrition =cut =head2 length Title : length Usage : my $len = $hit->length Function: Returns the length of the hit Returns : integer Args : [optional] integer to set the length =cut =head2 algorithm Title : algorithm Usage : $alg = $hit->algorithm(); Function: Gets the algorithm specification that was used to obtain the hit For BLAST, the algorithm denotes what type of sequence was aligned against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated dna-prt, TBLASTN prt-translated dna, TBLASTX translated dna-translated dna). Returns : a scalar string Args : [optional] scalar string to set the algorithm =cut =head2 raw_score Title : raw_score Usage : $score = $hit->raw_score(); Function: Gets the "raw score" generated by the algorithm. What this score is exactly will vary from algorithm to algorithm, returning undef if unavailable. Returns : a scalar value Args : [optional] scalar value to set the raw score =cut =head2 score Equivalent to L =cut =head2 significance Title : significance Usage : $significance = $hit->significance(); Function: Used to obtain the E or P value of a hit, i.e. the probability that this particular hit was obtained purely by random chance. If information is not available (nor calculatable from other information sources), return undef. Returns : a scalar value or undef if unavailable Args : [optional] scalar value to set the significance =cut =head2 bits Usage : $hit_object->bits(); Purpose : Gets the bit score of the best HSP for the current hit. Example : $bits = $hit_object->bits(); Returns : Integer or undef if bit score is not set Argument : n/a Comments : For BLAST1, the non-bit score is listed in the summary line. See Also : L =cut =head2 next_hsp Title : next_hsp Usage : while( $hsp = $obj->next_hsp()) { ... } Function : Returns the next available High Scoring Pair Example : Returns : Bio::Search::HSP::HSPI object or null if finished Args : none =cut =head2 hsps Usage : $hit_object->hsps(); Purpose : Get a list containing all HSP objects. : Get the numbers of HSPs for the current hit. Example : @hsps = $hit_object->hsps(); : $num = $hit_object->hsps(); # alternatively, use num_hsps() Returns : Array context : list of Bio::Search::HSP::BlastHSP.pm objects. : Scalar context: integer (number of HSPs). : (Equivalent to num_hsps()). Argument : n/a. Relies on wantarray Throws : Exception if the HSPs have not been collected. See Also : L, L =cut =head2 num_hsps Usage : $hit_object->num_hsps(); Purpose : Get the number of HSPs for the present hit. Example : $nhsps = $hit_object->num_hsps(); Returns : Integer or '-' if HSPs have not been callected Argument : n/a See Also : L =cut =head2 rewind Title : rewind Usage : $hit->rewind; Function: Allow one to reset the HSP iterator to the beginning Since this is an in-memory implementation Returns : none Args : none =cut =head2 ambiguous_aln Usage : $ambig_code = $hit_object->ambiguous_aln(); Purpose : Sets/Gets ambiguity code data member. Example : (see usage) Returns : String = 'q', 's', 'qs', '-' : 'q' = query sequence contains overlapping sub-sequences : while sbjct does not. : 's' = sbjct sequence contains overlapping sub-sequences : while query does not. : 'qs' = query and sbjct sequence contains overlapping sub-sequences : relative to each other. : '-' = query and sbjct sequence do not contains multiple domains : relative to each other OR both contain the same distribution : of similar domains. Argument : n/a Throws : n/a Comment : Note: "sbjct" is synonymous with "hit" =cut =head2 overlap See documentation in L =cut sub overlap { my $self = shift; if(@_) { $self->{'_overlap'} = shift; } defined $self->{'_overlap'} ? $self->{'_overlap'} : 0; } =head2 n Usage : $hit_object->n(); Purpose : Gets the N number for the current hit. : This is the number of HSPs in the set which was ascribed : the lowest P-value (listed on the description line). : This number is not the same as the total number of HSPs. : To get the total number of HSPs, use num_hsps(). Example : $n = $hit_object->n(); Returns : Integer Argument : n/a Throws : Exception if HSPs have not been set. Comments : Calling n() on such reports will result in a call to num_hsps(). : The num_hsps() method will count the actual number of : HSPs in the alignment listing, which may exceed N in : some cases. See Also : L =cut sub n { my $self = shift; # The check for $self->{'_n'} is a remnant from the 'query' mode days # in which the sbjct object would collect data from the description # line only. my ($n); if(not defined($self->{'_n'})) { if( $self->hsp ) { $n = $self->hsp->n; } } else { $n = $self->{'_n'}; } $n ||= $self->num_hsps; return $n; } =head2 p Usage : $hit_object->p( [format] ); Purpose : Get the P-value for the best HSP Example : $p = $sbjct->p; : $p = $sbjct->p('exp'); # get exponent only. : ($num, $exp) = $sbjct->p('parts'); # split sci notation into parts Returns : Float or scientific notation number (the raw P-value, DEFAULT). : Integer if format == 'exp' (the magnitude of the base 10 exponent). : 2-element list (float, int) if format == 'parts' and P-value : is in scientific notation (See Comments). Argument : format: string of 'raw' | 'exp' | 'parts' : 'raw' returns value given in report. Default. (1.2e-34) : 'exp' returns exponent value only (34) : 'parts' returns the decimal and exponent as a : 2-element list (1.2, -34) (See Comments). Throws : Warns if no P-value is defined. Uses expect instead. Comments : Using the 'parts' argument is not recommended since it will not : work as expected if the P-value is not in scientific notation. : That is, floats are not converted into sci notation before : splitting into parts. See Also : L, L, L =cut =head2 hsp Usage : $hit_object->hsp( [string] ); Purpose : Get a single HSPI object for the present HitI object. Example : $hspObj = $hit_object->hsp; # same as 'best' : $hspObj = $hit_object->hsp('best'); : $hspObj = $hit_object->hsp('worst'); Returns : Object reference for a Bio::Search::HSP::BlastHSP.pm object. Argument : String (or no argument). : No argument (default) = highest scoring HSP (same as 'best'). : 'best' or 'first' = highest scoring HSP. : 'worst' or 'last' = lowest scoring HSP. Throws : Exception if the HSPs have not been collected. : Exception if an unrecognized argument is used. See Also : L, L() =cut sub hsp { my( $self, $option ) = @_; $option ||= 'best'; if (not ref $self->{'_hsps'}) { $self->throw("Can't get HSPs: data not collected."); } my @hsps = $self->hsps; return $hsps[0] if $option =~ /best|first|1/i; return $hsps[$#hsps] if $option =~ /worst|last/i; $self->throw("Can't get HSP for: $option\n" . "Valid arguments: 'best', 'worst'"); } =head2 rank Title : rank Usage : $obj->rank($newval) Function: Get/Set the rank of this Hit in the Query search list i.e. this is the Nth hit for a specific query Returns : value of rank Args : newvalue (optional) =cut sub rank { my $self = shift; return $self->{'_rank'} = shift if @_; return $self->{'_rank'} || 1; } =head2 locus Title : locus Usage : $locus = $hit->locus(); Function: Retrieve the locus (if available) for the hit Returns : a scalar string (empty string if not set) Args : none =cut sub locus { my ($self,$value) = @_; my $previous = $self->{'_locus'}; if( defined $value || ! defined $previous ) { unless (defined $value) { if ($self->{'_name'} =~/(gb|emb|dbj|ref)\|(.*)\|(.*)/) { $value = $previous = $3; } else { $value = $previous = ''; } } $self->{'_locus'} = $value; } return $previous; } =head2 each_accession_number Title : each_accession_number Usage : @each_accession_number = $hit->each_accession_number(); Function: Get each accession number listed in the description of the hit. If there are no alternatives, then only the primary accession will be given Returns : list of all accession numbers in the description Args : none =cut sub each_accession_number { my ($self,$value) = @_; my $desc = $self->{'_description'}; #put primary accnum on the list my @accnums; push (@accnums,$self->{'_accession'}); if( defined $desc ) { while ($desc =~ /(\b\S+\|\S*\|\S*\s?)/g) { my $id = $1; my ($acc, $version); if ($id =~ /(gb|emb|dbj|sp|pdb|bbs|ref|tp[gde])\|(.*)\|(.*)/) { ($acc, $version) = split /\./, $2; } elsif ($id =~ /(pir|prf|pat|gnl)\|(.*)\|(.*)/) { ($acc, $version) = split /\./, $3; } elsif( $id =~ /(gim|gi|bbm|bbs|lcl)\|(\d*)/) { $acc = $id; } elsif( $id =~ /(oth)\|(.*)\|(.*)\|(.*)/ ) { # discontinued... ($acc,$version) = ($2); } else { #punt, not matching the db's at ftp://ftp.ncbi.nih.gov/blast/db/README #Database Name Identifier Syntax #============================ ======================== #GenBank gb|accession|locus #EMBL Data Library emb|accession|locus #DDBJ, DNA Database of Japan dbj|accession|locus #NBRF PIR pir||entry #Protein Research Foundation prf||name #SWISS-PROT sp|accession|entry name #Brookhaven Protein Data Bank pdb|entry|chain #Patents pat|country|number #GenInfo Backbone Id bbs|number #General database identifier gnl|database|identifier #NCBI Reference Sequence ref|accession|locus #Local Sequence identifier lcl|identifier $acc=$id; } push(@accnums, $acc); } } return @accnums; } =head2 tiled_hsps See documentation in L =cut =head2 query_length Title : query_length Usage : $obj->query_length($newval) Function: Get/Set the query_length Returns : value of query_length (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub query_length { my $self = shift; return $self->{'_query_length'} = shift if @_; return $self->{'_query_length'}; } =head2 ncbi_gi Title : ncbi_gi Usage : $acc = $hit->ncbi_gi(); Function: Retrieve the NCBI Unique ID (aka the GI #), if available, for the hit Returns : a scalar string (empty string if not set) Args : none =cut sub ncbi_gi { my ($self,$value) = @_; my $previous = $self->{'_ncbi_gi'}; if( defined $value || ! defined $previous ) { $value = $previous = '' unless defined $value; $self->{'_ncbi_gi'} = $value; } return $previous; } =head1 ModelHit methods overridden in ModelHit The following methods have been overridden due to their current reliance on sequence-based queries. They may be implemented in future versions of this class. =head2 length_aln =cut sub length_aln { my $self = shift; $self->warn('$hit->length_aln not implemented for Model-based searches'); return; } =head2 gaps =cut sub gaps { my $self = shift; $self->warn('$hit->gaps not implemented for Model-based searches'); return; } =head2 matches =cut sub matches { my $self = shift; $self->warn('$hit->matches not implemented for Model-based searches'); return; } =head2 start =cut sub start { my $self = shift; $self->warn('$hit->start not implemented for Model-based searches'); return; } =head2 end =cut sub end { my $self = shift; $self->warn('$hit->end not implemented for Model-based searches'); return; } =head2 range =cut sub range { my $self = shift; $self->warn('$hit->range not implemented for Model-based searches'); return; } =head2 frac_identical =cut sub frac_identical { my $self = shift; $self->warn('$hit->frac_identical not implemented for Model-based searches'); return; } =head2 frac_conserved =cut sub frac_conserved { my $self = shift; $self->warn('$hit->frac_conserved not implemented for Model-based searches'); return; } =head2 frac_aligned_query =cut sub frac_aligned_query { my $self = shift; $self->warn('$hit->frac_aligned_query not implemented for Model-based searches'); return; } =head2 frac_aligned_hit =cut sub frac_aligned_hit { my $self = shift; $self->warn('$hit->frac_aligned_hit not implemented for Model-based searches'); return; } =head2 num_unaligned_hit =cut *num_unaligned_sbjct = \&num_unaligned_hit; sub num_unaligned_hit { my $self = shift; $self->warn('$hit->num_unaligned_hit/num_unaligned_sbjct not implemented for Model-based searches'); return; } =head2 num_unaligned_query =cut sub num_unaligned_query { my $self = shift; $self->warn('$hit->num_unaligned_query not implemented for Model-based searches'); return; } =head2 seq_inds =cut sub seq_inds { my $self = shift; $self->warn('$hit->seq_inds not implemented for Model-based searches'); return; } =head2 strand =cut sub strand { my $self = shift; $self->warn('$hit->strand not implemented for Model-based searches'); return; } =head2 frame =cut sub frame { my $self = shift; $self->warn('$hit->frame not implemented for Model-based searches'); return; } =head2 logical_length =cut sub logical_length { my $self = shift; $self->warn('$hit->logical_length not implemented for Model-based searches'); return; } 1;