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Bio::Search::HSP::GenericHSP.3pm

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.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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

bioperl-l@bioperl.org

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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich and Steve Chervitz

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

CONTRIBUTORS

Sendu Bala, bix@sendu.me.uk

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 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)
            -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
 
 

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
 
 

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 ambiguous.  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
 
 

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
 
 

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)
 
 

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