Reference

Bio::Search::HSP::GenericHSP(3pm)

A "Generic" implementation of a High Scoring Pair

NAME

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

SYNOPSIS

    my $hsp = Bio::Search::HSP::GenericHSP->new( -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.

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 Bio::Search::HSP::HSPI.

FEEDBACK

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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.

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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich and Steve Chervitz

Email jason-at-bioperl.org Email sac-at-bioperl.org

CONTRIBUTORS

Sendu Bala, [email protected]

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $obj = Bio::Search::HSP::GenericHSP->new();
 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 comparisons;
                            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)
           -query_length=> total length of the query sequence
           -query_seq   => query sequence portion of the HSP
           -query_desc  => textual description of the query
           -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
           -hit_seq     => hit sequence portion of the HSP
           -hit_desc    => textual description of the hit
           -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)
           -hsp_group   => HSP Group informat (WU-BLAST only)
           -gap_symbol  => symbol representing a gap (default = '-')
           -hit_features=> string of features found in or near HSP hit
                           region (reported in some BLAST text output,
                           v. 2.2.13 and up)
           -stranded    => If the algorithm isn't known (i.e. defaults to
                           'generic'), setting this will indicate start/end
                           coordinates are to be used to determine the strand
                           for 'query', 'subject', 'hit', 'both', or 'none'
                           (default = 'none')

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 identical / length of alignment (with gaps)
                             synonyms: 'hsp'
                   default = 'total'
           arg 2: [optional] frac identical value to set for the type requested
 Note    : for translated sequences, this adjusts the length accordingly

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 gap characters in the query, hit, or total alignment.
 Returns  : Integer, number of gaps or 0 if none
 Args     : arg 1: 'query' = num gap characters in query seq
                   'hit'   = num gap characters in hit seq; synonyms: 'sbjct', 'subject'
                   'total' = num gap characters 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

consensus_string

 Title   : consensus_string
 Usage   : my $cs_string = $hsp->consensus_string;
 Function: Retrieves the consensus structure line for this HSP as a string (HMMER).
         : If the model had any consensus structure or reference line annotation
         : that it inherited from a multiple alignment (#=GC SS cons,
         : #=GC RF annotation in Stockholm files), that information is shown
         : as CS or RF annotation line.
 Returns : string
 Args    : [optional] string to set for consensus structure

posterior_string

 Title   : posterior_string
 Usage   : my $pp_string = $hsp->posterior_string;
 Function: Retrieves the posterior probability line for this HSP as a string (HMMer3).
         : The posterior probability is the string of symbols at the bottom
         : of the alignment indicating the expected accuracy of each aligned residue.
         : A 0 means 0-5%, 1 means 5-15%, and so on; 9 means 85-95%,
         : and a * means 95-100% posterior probability.
 Returns : string
 Args    : [optional] string to set for posterior probability

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   : my ($qframe, $hframe) = $hsp->frame('list',$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 subject frame if return type wants an array
           or query frame if defined or subject frame if not defined
 Args    : 'hit' or 'subject' or 'sbjct' to retrieve the frame of the subject (default)
           'query' to retrieve the query frame 
           'list' or 'array' to retrieve both query and hit frames together
 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 : integer
 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' - identical positions
           :             'conserved' - conserved positions
           :             'nomatch'   - mismatched residue or gap positions
           :             'mismatch'  - mismatched residue positions (no gaps)
           :             'gap'       - gap positions only
           :             'frameshift'- frameshift positions only
           :             'conserved-not-identical' - conserved positions w/o 
           :                            identical residues
           :             The name can be shortened to 'id' or 'cons' unless
           :             the name is .  The default value is
           :             '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  : For HSPs partially or completely derived from translated sequences
           : (TBLASTN, BLASTX, TBLASTX, or similar), some positional data
           : cannot easily be attributed to a single position (i.e. the 
           : positional data is ambiguous).  In these cases all three codon 
           : positions are reported.  Under these conditions you can check 
           : ambiguous_seq_inds() to determine whether the query, subject, 
           : or both are ambiguous.
           :
See Also   : L<Bio::Search::SearchUtils::collapse_nums()|Bio::Search::SearchUtils>,
             L<Bio::Search::Hit::HitI::seq_inds()|Bio::Search::Hit::HitI>

ambiguous_seq_inds

 Title     : ambiguous_seq_inds
 Purpose   : returns a string denoting whether sequence indices for query, 
           : subject, or both are ambiguous
 Returns   : String; 'query', 'subject', 'query/subject', or empty string ''
 Argument  : none
 Comments  : For HSPs partially or completely derived from translated sequences
           : (TBLASTN, BLASTX, TBLASTX, or similar), some positional data
           : cannot easily be attributed to a single position (i.e. the 
           : positional data is ambiguous).  In these cases all three codon 
           : positions are reported when using seq_inds().  Under these
           : conditions you can check ambiguous_seq_inds() to determine whether
           : the query, subject, or both are ambiguous.
See Also   : L<Bio::Search::Hit::HSPI::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

strand

 Title   : strand
 Usage   : $hsp->strand('query')
 Function: Retrieves the strand for the HSP component requested
 Returns : +1 or -1
 Args    : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject,
           'query' to retrieve the query strand (default)

score

 Title   : score
 Usage   : $score = $obj->score();
           $obj->score($value);
 Function: Get/Set the score 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

Private methods

_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)

hsp_group

 Title   : hsp_group
 Usage   : $obj->hsp_group($newval)
 Function: Get/Set the Group value (from WU-BLAST)
           Indicates a grouping of HSPs
 Returns : Value of group
 Args    : On set, new value (a scalar or undef, optional)

hit_features

 Title   : hit_features
 Usage   : $obj->hit_features($newval)
 Function: Get/Set the HSP hit feature string (from some BLAST 2.2.13 text
           output), which is a string of overlapping or nearby features in HSP
           hit
 Returns : Value of hit features, if present
 Args    : On set, new value (a scalar or undef, optional)

Brief introduction on cigar string

NOTE: the concept is originally from EnsEMBL docs at http://may2005.archive.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

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