Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair 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. 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 Bio::Search::HSP::HSPI.

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

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/ Email jason@bioperl.org Email sac@bioperl.org Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Bio::Search::HSP::HSPI methods
Implementation of Bio::Search::HSP::HSPI methods follow

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

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

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

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

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

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

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

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

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

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

hsp_length
Title : hsp_length Usage : my $len = $hsp->hsp_length() Function: shortcut length('hsp') Returns : floating point between 0 and 100 Args : none

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

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)

get_aln
Title : get_aln Usage : my $aln = $hsp->gel_aln Function: Returns a L<Bio::SimpleAlign> object representing the HSP alignment Returns : L<Bio::SimpleAlign> Args : none

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)

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)

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.

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 : Bio::Search::SearchUtils::collapse_nums(), Bio::Search::Hit::HitI::seq_inds()

Inherited from Bio::SeqFeature::SimilarityPair
These methods come from Bio::SeqFeature::SimilarityPair

query
Title : query Usage : my $query = $hsp->query Function: Returns a SeqFeature representing the query in the HSP Returns : L<Bio::SeqFeature::Similarity> Args : [optional] new value to set

hit
Title : hit Usage : my $hit = $hsp->hit Function: Returns a SeqFeature representing the hit in the HSP Returns : L<Bio::SeqFeature::Similarity> Args : [optional] new value to set

significance
Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Get/Set the significance value Returns : numeric Args : [optional] new value to set

bits
Title : bits Usage : $bits = $obj->bits(); $obj->bits($value); Function: Get/Set the bits value Returns : numeric Args : [optional] new value to set

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)

_calculate_seq_positions
Title : _calculate_seq_positions Usage : $self->_calculate_seq_positions Function: Internal function Returns : Args :

n
See documentation in Bio::Search::HSP::HSPI::n()

range
See documentation in Bio::Search::HSP::HSPI::range()

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) 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

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

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