Start and End coordinates

•

Supports BLAST versions 1.x and 2.x, gapped and ungapped.

Bio::Search::HSP::PsiBlastHSP.pm has the ability to extract a list of all residue indices for identical and conservative matches along both query and sbjct sequences. Since this degree of detail is not always needed, this behavior does not occur during construction of the PsiBlastHSP object. These data will automatically be collected as necessary as the PsiBlastHSP.pm object is used.

Relationship to Bio::SimpleAlign and Bio::Seq

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Support

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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

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

Links:

 http://bio.perl.org/                       - Bioperl Project Homepage

new

 Usage     : $hsp = Bio::Search::HSP::PsiBlastHSP->new( %named_params );
           : Bio::Search::HSP::PsiBlastHSP.pm objects are constructed
           : automatically by Bio::SearchIO::BlastHitFactory.pm,
           : so there is no need for direct instantiation.
 Purpose   : Constructs a new PsiBlastHSP object and Initializes key variables
           : for the HSP.
 Returns   : A Bio::Search::HSP::PsiBlastHSP object
 Argument  : Named parameters:
           : Parameter keys are case-insensitive.
           :      -RAW_DATA  => array ref containing raw BLAST report data for
           :                    for a single HSP. This includes all lines
           :                    of the HSP alignment from a traditional BLAST
                                or PSI-BLAST (non-XML) report,
           :      -RANK         => integer (1..n).
           :      -PROGRAM      => string ('TBLASTN', 'BLASTP', etc.).
           :      -QUERY_NAME   => string, id of query sequence
           :      -HIT_NAME     => string, id of hit sequence
           :
 Comments  : Having the raw data allows this object to do lazy parsing of
           : the raw HSP data (i.e., not parsed until needed).
           :
           : Note that there is a fair amount of basic parsing that is
           : currently performed in this module that would be more appropriate
           : to do within a separate factory object.
           : This parsing code will likely be relocated and more initialization
           : parameters will be added to new().
           :
See Also   : L<Bio::SeqFeature::SimilarityPair::new()>, L<Bio::SeqFeature::Similarity::new()>

algorithm

 Title   : algorithm
 Usage   : $alg = $hsp->algorithm();
 Function: Gets the algorithm specification that was used to obtain the hsp
           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    : none

signif()

 Usage     : $hsp_obj->signif()
 Purpose   : Get the P-value or Expect value for the HSP.
 Returns   : Float (0.001 or 1.3e-43)
           : Returns P-value if it is defined, otherwise, Expect value.
 Argument  : n/a
 Throws    : n/a
 Comments  : Provided for consistency with BlastHit::signif()
           : Support for returning the significance data in different
           : formats (e.g., exponent only), is not provided for HSP objects.
           : This is only available for the BlastHit or Blast object.

See Also : "p", "expect", Bio::Search::Hit::BlastHit::signif()

evalue

 Usage     : $hsp_obj->evalue()
 Purpose   : Get the Expect value for the HSP.
 Returns   : Float (0.001 or 1.3e-43)
 Argument  : n/a
 Throws    : n/a
 Comments  : Support for returning the expectation data in different
           : formats (e.g., exponent only), is not provided for HSP objects.
           : This is only available for the BlastHit or Blast object.

See Also : "p"

p

 Usage     : $hsp_obj->p()
 Purpose   : Get the P-value for the HSP.
 Returns   : Float (0.001 or 1.3e-43) or undef if not defined.
 Argument  : n/a
 Throws    : n/a
 Comments  : P-value is not defined with NCBI Blast2 reports.
           : Support for returning the expectation data in different
           : formats (e.g., exponent only) is not provided for HSP objects.
           : This is only available for the BlastHit or Blast object.

See Also : "expect"

length

 Usage     : $hsp->length( [seq_type] )
 Purpose   : Get the length of the aligned portion of the query or sbjct.
 Example   : $hsp->length('query')
 Returns   : integer
 Argument  : seq_type: 'query' | 'hit' or 'sbjct' | 'total'  (default = 'total')
             ('sbjct' is synonymous with 'hit')
 Throws    : n/a
 Comments  : 'total' length is the full length of the alignment
           : as reported in the denominators in the alignment section:
           : "Identical = 34/120 Positives = 67/120".

See Also : "gaps"

gaps

 Usage     : $hsp->gaps( [seq_type] )
 Purpose   : Get the number of gap characters in the query, sbjct, or total alignment.
           : Also can return query gap chars and sbjct gap chars as a two-element list
           : when in array context.
 Example   : $total_gaps      = $hsp->gaps();
           : ($qgaps, $sgaps) = $hsp->gaps();
           : $qgaps           = $hsp->gaps('query');
 Returns   : scalar context: integer
           : array context without args: (int, int) = ('queryGaps', 'sbjctGaps')
 Argument  : seq_type: 'query' or 'hit' or 'sbjct' or 'total'
           :  ('sbjct' is synonymous with 'hit')
           : (default = 'total', scalar context)
           : Array context can be "induced" by providing an argument of 'list' or 'array'.
 Throws    : n/a

See Also : "length", "matches"

frac_identical

 Usage     : $hsp_object->frac_identical( [seq_type] );
 Purpose   : Get the fraction of identical positions within the given HSP.
 Example   : $frac_iden = $hsp_object->frac_identical('query');
 Returns   : Float (2-decimal precision, e.g., 0.75).
 Argument  : seq_type: 'query' or 'hit' or 'sbjct' or 'total'
           :  ('sbjct' is synonymous with 'hit')
           : default = 'total' (but see comments below).
 Throws    : n/a
 Comments  : Different versions of Blast report different values for the total
           : length of the alignment. This is the number reported in the
           : denominators in the stats section:
           : "Identical = 34/120 Positives = 67/120".
           : NCBI-BLAST uses the total length of the alignment (with gaps)
           : WU-BLAST uses the length of the query sequence (without gaps).
           : Therefore, when called without an argument or an argument of 'total',
           : this method will report different values depending on the
           : version of BLAST used.
           :
           : To get the fraction identical among only the aligned residues,
           : ignoring the gaps, call this method with an argument of 'query'
           : or 'sbjct' ('sbjct' is synonymous with 'hit').

See Also : "frac_conserved", "num_identical", "matches"

frac_conserved

 Usage     : $hsp_object->frac_conserved( [seq_type] );
 Purpose   : Get the fraction of conserved positions within the given HSP.
           : (Note: 'conservative' positions are called 'positives' in the
           : Blast report.)
 Example   : $frac_cons = $hsp_object->frac_conserved('query');
 Returns   : Float (2-decimal precision, e.g., 0.75).
 Argument  : seq_type: 'query' or 'hit' or 'sbjct' or 'total'
           :  ('sbjct' is synonymous with 'hit')
           : default = 'total' (but see comments below).
 Throws    : n/a
 Comments  : Different versions of Blast report different values for the total
           : length of the alignment. This is the number reported in the
           : denominators in the stats section:
           : "Identical = 34/120 Positives = 67/120".
           : NCBI-BLAST uses the total length of the alignment (with gaps)
           : WU-BLAST uses the length of the query sequence (without gaps).
           : Therefore, when called without an argument or an argument of 'total',
           : this method will report different values depending on the
           : version of BLAST used.
           :
           : To get the fraction conserved among only the aligned residues,
           : ignoring the gaps, call this method with an argument of 'query'
           : or 'sbjct'.

See Also : "frac_conserved", "num_conserved", "matches"

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

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

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

expect

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.

to_string

 Title   : to_string
 Usage   : print $hsp->to_string;
 Function: Returns a string representation for the Blast HSP.
           Primarily intended for debugging purposes.
 Example : see usage
 Returns : A string of the form:
           [PsiBlastHSP] <rank>
           e.g.:
           [BlastHit] 1
 Args    : None

_set_data

 Usage     : called automatically during object construction.
 Purpose   : Parses the raw HSP section from a flat BLAST report and
             sets the query sequence, sbjct sequence, and the "match" data
           : which consists of the symbols between the query and sbjct lines
           : in the alignment.
 Argument  : Array (all lines for a single, complete HSP, from a raw,
             flat (i.e., non-XML) BLAST report)
 Throws    : Propagates any exceptions from the methods called ("See Also")

See Also : "_set_seq", "_set_score_stats", "_set_match_stats"

_set_score_stats

 Usage     : called automatically by _set_data()
 Purpose   : Sets various score statistics obtained from the HSP listing.
 Argument  : String with any of the following formats:
           : blast2:  Score = 30.1 bits (66), Expect = 9.2
           : blast2:  Score = 158.2 bits (544), Expect(2) = e-110
           : blast1:  Score = 410 (144.3 bits), Expect = 1.7e-40, P = 1.7e-40
           : blast1:  Score = 55 (19.4 bits), Expect = 5.3, Sum P(3) = 0.99
 Throws    : Exception if the stats cannot be parsed, probably due to a change
           : in the Blast report format.

See Also : "_set_data"

_set_match_stats

 Usage     : Private method; called automatically by _set_data()
 Purpose   : Sets various matching statistics obtained from the HSP listing.
 Argument  : blast2: Identities = 23/74 (31%), Positives = 29/74 (39%), Gaps = 17/74 (22%)
           : blast2: Identities = 57/98 (58%), Positives = 74/98 (75%)
           : blast1: Identities = 87/204 (42%), Positives = 126/204 (61%)
           : blast1: Identities = 87/204 (42%), Positives = 126/204 (61%), Frame = -3
           : WU-blast: Identities = 310/553 (56%), Positives = 310/553 (56%), Strand = Minus / Plus
 Throws    : Exception if the stats cannot be parsed, probably due to a change
           : in the Blast report format.
 Comments  : The "Gaps = " data in the HSP header has a different meaning depending
           : on the type of Blast: for BLASTP, this number is the total number of
           : gaps in query+sbjct; for TBLASTN, it is the number of gaps in the
           : query sequence only. Thus, it is safer to collect the data
           : separately by examining the actual sequence strings as is done
           : in _set_seq().

See Also : "_set_data", "_set_seq"

_set_seq_data

 Usage     : called automatically when sequence data is requested.
 Purpose   : Sets the HSP sequence data for both query and sbjct sequences.
           : Includes: start, stop, length, gaps, and raw sequence.
 Argument  : n/a
 Throws    : Propagates any exception thrown by _set_match_seq()
 Comments  : Uses raw data stored by _set_data() during object construction.
           : These data are not always needed, so it is conditionally
           : executed only upon demand by methods such as gaps(), _set_residues(),
           : etc. _set_seq() does the dirty work.

See Also : "_set_seq"

_set_seq

 Usage     : called automatically by _set_seq_data()
           : $hsp_obj->($seq_type, @data);
 Purpose   : Sets sequence information for both the query and sbjct sequences.
           : Directly counts the number of gaps in each sequence (if gapped Blast).
 Argument  : $seq_type = 'query' or 'sbjct'
           : @data = all seq lines with the form:
           : Query: 61  SPHNVKDRKEQNGSINNAISPTATANTSGSQQINIDSALRDRSSNVAAQPSLSDASSGSN 120
 Throws    : Exception if data strings cannot be parsed, probably due to a change
           : in the Blast report format.
 Comments  : Uses first argument to determine which data members to set
           : making this method sensitive data member name changes.
           : Behavior is dependent on the type of BLAST analysis (TBLASTN, BLASTP, etc).
 Warning   : Sequence endpoints are normalized so that start < end. This affects HSPs
           : for TBLASTN/X hits on the minus strand. Normalization facilitates use
           : of range information by methods such as match().

See Also : "_set_seq_data", "matches", "range", "start", "end"

_set_residues

 Usage     : called automatically when residue data is requested.
 Purpose   : Sets the residue numbers representing the identical and
           : conserved positions. These data are obtained by analyzing the
           : symbols between query and sbjct lines of the alignments.
 Argument  : n/a
 Throws    : Propagates any exception thrown by _set_seq_data() and _set_match_seq().
 Comments  : These data are not always needed, so it is conditionally
           : executed only upon demand by methods such as seq_inds().
           : Behavior is dependent on the type of BLAST analysis (TBLASTN, BLASTP, etc).

See Also : "_set_seq_data", "_set_match_seq", "seq_inds"

_set_match_seq

 Usage     : $hsp_obj->_set_match_seq()
 Purpose   : Set the 'match' sequence for the current HSP (symbols in between
           : the query and sbjct lines.)
 Returns   : Array reference holding the match sequences lines.
 Argument  : n/a
 Throws    : Exception if the _matchList field is not set.
 Comments  : The match information is not always necessary. This method
           : allows it to be conditionally prepared.
           : Called by _set_residues>() and seq_str().

See Also : "_set_residues", "seq_str"

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::BlastHit::num_hsps().

See Also : Bio::SeqFeature::SimilarityPair::score()

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 : "length", "gaps", "seq_str", Bio::Search::Hit::BlastHit::_adjust_contigs()

num_identical

 Usage     : $hsp_object->num_identical();
 Purpose   : Get the number of identical positions within the given HSP.
 Example   : $num_iden = $hsp_object->num_identical();
 Returns   : integer
 Argument  : n/a
 Throws    : n/a

See Also : "num_conserved", "frac_identical"

num_conserved

 Usage     : $hsp_object->num_conserved();
 Purpose   : Get the number of conserved positions within the given HSP.
 Example   : $num_iden = $hsp_object->num_conserved();
 Returns   : integer
 Argument  : n/a
 Throws    : n/a

See Also : "num_identical", "frac_conserved"

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

See Also : "start", "end"

start

 Usage     : $hsp->start( [seq_type] );
 Purpose   : Gets the start coordinate for the query, sbjct, or both sequences
           : in the HSP alignment.
           : NOTE: Start will always be less than end.
           : To determine strand, use $hsp->strand()
 Example   : $query_beg = $hsp->start('query');
           : $hit_beg = $hsp->start('hit');
           : ($query_beg, $hit_beg) = $hsp->start();
 Returns   : scalar context: integer
           : array context without args: list of two integers
 Argument  : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default= 'query')
           :  ('sbjct' is synonymous with 'hit')
           : Array context can be "induced" by providing an argument of 'list' or 'array'.
 Throws    : n/a

See Also : "end", "range"

end

 Usage     : $hsp->end( [seq_type] );
 Purpose   : Gets the end coordinate for the query, sbjct, or both sequences
           : in the HSP alignment.
           : NOTE: Start will always be less than end.
           : To determine strand, use $hsp->strand()
 Example   : $query_end = $hsp->end('query');
           : $hit_end = $hsp->end('hit');
           : ($query_end, $hit_end) = $hsp->end();
 Returns   : scalar context: integer
           : array context without args: list of two integers
 Argument  : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default= 'query')
           :  ('sbjct' is synonymous with 'hit')
           : Array context can be "induced" by providing an argument of 'list' or 'array'.
 Throws    : n/a

See Also : "start", "range", "strand"

strand

 Usage     : $hsp_object->strand( [seq_type] )
 Purpose   : Get the strand of the query or sbjct sequence.
 Example   : print $hsp->strand('query');
           : ($query_strand, $hit_strand) = $hsp->strand();
 Returns   : -1, 0, or 1
           : -1 = Minus strand, +1 = Plus strand
           : Returns 0 if strand is not defined, which occurs
           : for BLASTP reports, and the query of TBLASTN
           : as well as the hit if BLASTX reports.
           : In scalar context without arguments, returns queryStrand value.
           : In array context without arguments, returns a two-element list
           :    of strings (queryStrand, sbjctStrand).
           : Array context can be "induced" by providing an argument of 'list' or 'array'.
 Argument  : seq_type: 'query' or 'hit' or 'sbjct' or undef
           :  ('sbjct' is synonymous with 'hit')
 Throws    : n/a

See Also : "_set_seq", "_set_match_stats"

seq

 Usage     : $hsp->seq( [seq_type] );
 Purpose   : Get the query or sbjct sequence as a Bio::Seq.pm object.
 Example   : $seqObj = $hsp->seq('query');
 Returns   : Object reference for a Bio::Seq.pm object.
 Argument  : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query').
           :  ('sbjct' is synonymous with 'hit')
 Throws    : Propagates any exception that occurs during construction
           : of the Bio::Seq.pm object.
 Comments  : The sequence is returned in an array of strings corresponding
           : to the strings in the original format of the Blast alignment.
           : (i.e., same spacing).

See Also : "seq_str", "seq_inds", Bio::Seq

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')
 Throws    : Exception if the argument does not match an accepted seq_type.
 Comments  : Calls _set_seq_data() to set the 'match' sequence if it has
           : not been set already.

See Also : "seq", "seq_inds", "_set_match_seq"

seq_inds

 Usage     : $hsp->seq_inds( seq_type, class, collapse );
 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' (default = identical)
           :              (can be shortened to 'id' or 'cons')
           :              (actually, anything not 'id' will evaluate to 'conserved').
           : 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  : Calls _set_residues() to set the 'match' sequence if it has
           : not been set already.

See Also : "seq", "_set_residues", Bio::Search::BlastUtils::collapse_nums(), Bio::Search::Hit::BlastHit::seq_inds()

get_aln

 Usage     : $hsp->get_aln()
 Purpose   : Get a Bio::SimpleAlign object constructed from the query + sbjct
           : sequences of the present HSP object.
 Example   : $aln_obj = $hsp->get_aln();
 Returns   : Object reference for a Bio::SimpleAlign.pm object.
 Argument  : n/a.
 Throws    : Propagates any exception ocurring during the construction of
           : the Bio::SimpleAlign object.
 Comments  : Requires Bio::SimpleAlign.
           : The Bio::SimpleAlign object is constructed from the query + sbjct
           : sequence objects obtained by calling seq().
           : Gap residues are included (see $GAP_SYMBOL).

See Also : "seq", Bio::SimpleAlign

Data Members

1 Do NOT rely on these in any code outside of this module.

All data members are prefixed with an underscore to signify that they are private. Always use accessor methods. If the accessor doesn't exist or is inadequate, create or modify an accessor (and let me know, too!).

2 This documentation may be incomplete and out of date.

It is easy for these data member descriptions to become obsolete as this module is still evolving. Always double check this info and search for members not described here.

An instance of Bio::Search::HSP::PsiBlastHSP.pm is a blessed reference to a hash containing all or some of the following fields:

 FIELD           VALUE
 --------------------------------------------------------------
 (member names are mostly self-explanatory)

 _score              :
 _bits               :
 _p                  :
 _n                  : Integer. The 'N' value listed in parenthesis with P/Expect value:
                     : e.g., P(3) = 1.2e-30  ---> (N = 3).
                     : Not defined in NCBI Blast2 with gaps.
                     : To obtain the number of HSPs, use Bio::Search::Hit::BlastHit::num_hsps().
 _expect             :
 _queryLength        :
 _queryGaps          :
 _queryStart         :
 _queryStop          :
 _querySeq           :
 _sbjctLength        :
 _sbjctGaps          :
 _sbjctStart         :
 _sbjctStop          :
 _sbjctSeq           :
 _matchSeq           : String. Contains the symbols between the query and sbjct lines
                       which indicate identical (letter) and conserved ('+') matches
                       or a mismatch (' ').
 _numIdentical       :
 _numConserved       :
 _identicalRes_query :
 _identicalRes_sbjct :
 _conservedRes_query :
 _conservedRes_sbjct :
 _match_indent       : The number of leading space characters on each line containing
                       the match symbols. _match_indent is 13 in this example:
                         Query:   285 QNSAPWGLARISHRERLNLGSFNKYLYDDDAG
                                      Q +APWGLARIS       G+ + Y YD+ AG
                         ^^^^^^^^^^^^^