The rest of the documentation details each of the object methods. Internal methods are usually preceded
with a _
new
Usage : $hit = Bio::Search::Hit::PsiBlastHit->new( %named_params );
: Bio::Search::Hit::PsiBlastHit.pm objects are constructed
: automatically by Bio::SearchIO::PsiBlastHitFactory.pm,
: so there is no need for direct instantiation.
Purpose : Constructs a new PsiBlastHit object and Initializes key variables
: for the hit.
Returns : A Bio::Search::Hit::PsiBlastHit object
Argument : Named Parameters:
: Parameter keys are case-insensitive.
: -RAW_DATA => array reference holding raw BLAST report data
: for a single hit. This includes all lines
: within the HSP alignment listing section of a
: traditional BLAST or PSI-BLAST (non-XML) report,
: starting at (or just after) the leading '>'.
: -HOLD_RAW_DATA => boolean, should -RAW_DATA be saved within the object.
: -QUERY_LEN => Length of the query sequence
: -ITERATION => integer (PSI-BLAST iteration number in which hit was found)
: -OVERLAP => integer (maximum overlap between adjacent
: HSPs when tiling)
: -PROGRAM => string (type of Blast: BLASTP, BLASTN, etc)
: -SIGNIF => significance
: -IS_PVAL => boolean, true if -SIGNIF contains a P-value
: -SCORE => raw BLAST score
: -FOUND_AGAIN => boolean, true if this was a hit from the
: section of a PSI-BLAST with iteration > 1
: containing sequences that were also found
: in iteration 1.
Comments : This object accepts raw Blast report data not because it
: is required for parsing, but in order to retrieve it
: (only available if -HOLD_RAW_DATA is set to true).
See Also : Bio::Search::BlastUtils::tile_hsps(), Bio::Root::Root::new()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 : none
name
Usage : $hit->name([string]);
Purpose : Set/Get a string to identify the hit.
Example : $name = $hit->name;
: $hit->name('M81707');
Returns : String consisting of the hit's name or undef if not set.
Comments : The name is parsed out of the "Query=" line as the first chunk of
non-whitespace text. If you want the rest of the line, use
$hit->description().
See Also: accession()description
Usage : $hit_object->description( [integer] );
Purpose : Set/Get a description string for the hit.
This is parsed out of the "Query=" line as everything after
the first chunk of non-whitespace text. Use $hit->name()
to get the first chunk (the ID of the sequence).
Example : $description = $hit->description;
: $desc_60char = $hit->description(60);
Argument : Integer (optional) indicating the desired length of the
: description string to be returned.
Returns : String consisting of the hit's description or undef if not set.
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
Comments: Accession numbers are extracted based on the assumption that they
are delimited by | characters (NCBI-style). If this is not the case,
use the name() method and parse it as necessary.
See Also: name()raw_score
Usage : $hit_object->raw_score();
Purpose : Gets the BLAST score of the best HSP for the current Blast hit.
Example : $score = $hit_object->raw_score();
Returns : Integer
Argument : n/a
Throws : n/a
See Also : bits()length
Usage : $hit_object->length();
Purpose : Get the total length of the hit sequence.
Example : $len = $hit_object->length();
Returns : Integer
Argument : n/a
Throws : n/a
Comments : Developer note: when using the built-in length function within
: this module, call it as CORE::length().
See Also : logical_length(), length_aln()significance
Equivalent to signif()next_hsp
Title : next_hsp
Usage : $hsp = $obj->next_hsp();
Function : returns the next available High Scoring Pair object
Example :
Returns : Bio::Search::HSP::BlastHSP or undef if finished
Args : none
score
Equivalent to raw_score()hit_length
Equivalent to length()signif
Usage : $hit_object->signif( [format] );
Purpose : Get the P or Expect value for the best HSP of the given BLAST hit.
: The value returned is the one which is reported in the description
: section of the Blast report. For Blast1 and WU-Blast2, this
: is a P-value, for Blast2, it is an Expect value.
Example : $obj->signif() # returns 1.3e-34
: $obj->signif('exp') # returns -34
: $obj->signif('parts') # returns (1.3, -34)
Returns : Float or scientific notation number (the raw P/Expect value, DEFAULT).
: Integer if format == 'exp' (the magnitude of the base 10 exponent).
: 2-element list (float, int) if format == 'parts' and P/Expect 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 : n/a
Comments : The signif() method provides a way to deal with the fact that
: Blast1 and Blast2 formats (and WU- vs. NCBI-BLAST) differ in
: what is reported in the description lines of each hit in the
: Blast report. The signif() method frees any client code from
: having to know if this is a P-value or an Expect value,
: making it easier to write code that can process both
: Blast1 and Blast2 reports. This is not necessarily a good thing,
: since one should always know when one is working with P-values or
: Expect values (hence the deprecated status).
: Use of expect() is recommended since all hits will have an Expect value.
:
: Using the 'parts' argument is not recommended since it will not
: work as expected if the expect value is not in scientific notation.
: That is, floats are not converted into sci notation before
: splitting into parts.
See Also : p(), expect(), Bio::Search::BlastUtils::get_exponent()to_string
Title : to_string
Usage : print $hit->to_string;
Function: Returns a string representation for the Blast Hit.
Primarily intended for debugging purposes.
Example : see usage
Returns : A string of the form:
[PsiBlastHit] <name> <description>
e.g.:
[PsiBlastHit] emb|Z46660|SC9725 S.cerevisiae chromosome XIII cosmid
Args : None
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
Status : Experimental
See Also : Bio::Search::BlastUtils::tile_hsps, "HSP Tiling and Ambiguous Alignments"
overlap
Usage : $blast_object->overlap( [integer] );
Purpose : Gets/Sets the allowable amount overlap between different HSP sequences.
Example : $blast_object->overlap(5);
: $overlap = $blast_object->overlap;
Returns : Integer.
Argument : integer.
Throws : n/a
Status : Experimental
Comments : Any two HSPs whose sequences overlap by less than or equal
: to the overlap() number of resides will be considered separate HSPs
: and will not get tiled by Bio::Search::BlastUtils::_adjust_contigs().
See Also : Bio::Search::BlastUtils::_adjust_contigs(), BUGS
bits
Usage : $hit_object->bits();
Purpose : Gets the BLAST bit score of the best HSP for the current Blast hit.
Example : $bits = $hit_object->bits();
Returns : Integer
Argument : n/a
Throws : Exception if bit score is not set.
Comments : For BLAST1, the non-bit score is listed in the summary line.
See Also : score()n
Usage : $hit_object->n();
Purpose : Gets the N number for the current Blast 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 (BLAST2 reports).
Comments : Note that the N parameter is not reported in gapped BLAST2.
: 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 : num_hsps()frame
Usage : $hit_object->frame();
Purpose : Gets the reading frame for the best HSP after HSP tiling.
: This is only valid for BLASTX and TBLASTN/X reports.
Example : $frame = $hit_object->frame();
Returns : Integer (-2 .. +2)
Argument : n/a
Throws : Exception if HSPs have not been set (BLAST2 reports).
Comments : This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically..
: If you don't want the tiled data, iterate through each HSP
: calling frame() on each (use hsps() to get all HSPs).
See Also : hsps()p
Usage : $hit_object->p( [format] );
Purpose : Get the P-value for the best HSP of the given BLAST hit.
: (Note that P-values are not provided with NCBI Blast2 reports).
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 : expect(), signif(), Bio::Search::BlastUtils::get_exponent()expect
Usage : $hit_object->expect( [format] );
Purpose : Get the Expect value for the best HSP of the given BLAST hit.
Example : $e = $sbjct->expect;
: $e = $sbjct->expect('exp'); # get exponent only.
: ($num, $exp) = $sbjct->expect('parts'); # split sci notation into parts
Returns : Float or scientific notation number (the raw expect value, DEFAULT).
: Integer if format == 'exp' (the magnitude of the base 10 exponent).
: 2-element list (float, int) if format == 'parts' and Expect
: 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 : Exception if the Expect value is not defined.
Comments : Using the 'parts' argument is not recommended since it will not
: work as expected if the expect value is not in scientific notation.
: That is, floats are not converted into sci notation before
: splitting into parts.
See Also : p(), signif(), Bio::Search::BlastUtils::get_exponent()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 : hsp(), num_hsps()hsp
Usage : $hit_object->hsp( [string] );
Purpose : Get a single BlastHSP.pm object for the present PsiBlastHit.pm 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 : hsps(), num_hsps()
num_hsps
Usage : $hit_object->num_hsps();
Purpose : Get the number of HSPs for the present Blast hit.
Example : $nhsps = $hit_object->num_hsps();
Returns : Integer
Argument : n/a
Throws : Exception if the HSPs have not been collected.
See Also : hsps()logical_length
Usage : $hit_object->logical_length( [seq_type] );
: (mostly intended for internal use).
Purpose : Get the logical length of the hit sequence.
: For query sequence of BLASTX and TBLASTX reports and the hit
: sequence of TBLASTN and TBLASTX reports, the returned length
: is the length of the would-be amino acid sequence (length/3).
: For all other BLAST flavors, this function is the same as length().
Example : $len = $hit_object->logical_length();
Returns : Integer
Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query')
('sbjct' is synonymous with 'hit')
Throws : n/a
Comments : This is important for functions like frac_aligned_query()
: which need to operate in amino acid coordinate space when dealing
: with T?BLASTX type reports.
See Also : length(), frac_aligned_query(), frac_aligned_hit()length_aln
Usage : $hit_object->length_aln( [seq_type] );
Purpose : Get the total length of the aligned region for query or sbjct seq.
: This number will include all HSPs
Example : $len = $hit_object->length_aln(); # default = query
: $lenAln = $hit_object->length_aln('query');
Returns : Integer
Argument : seq_Type = 'query' or 'hit' or 'sbjct' (Default = 'query')
('sbjct' is synonymous with 'hit')
Throws : Exception if the argument is not recognized.
Comments : This method will report the logical length of the alignment,
: meaning that for TBLAST[NX] reports, the length is reported
: using amino acid coordinate space (i.e., nucleotides / 3).
:
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically..
: If you don't want the tiled data, iterate through each HSP
: calling length() on each (use hsps() to get all HSPs).
See Also : length(), frac_aligned_query(), frac_aligned_hit(), gaps(),
Bio::Search::BlastUtils::tile_hsps(), Bio::Search::HSP::BlastHSP::length()gaps
Usage : $hit_object->gaps( [seq_type] );
Purpose : Get the number of gaps in the aligned query, sbjct, or both sequences.
: Data is summed across all HSPs.
Example : $qgaps = $hit_object->gaps('query');
: $hgaps = $hit_object->gaps('hit');
: $tgaps = $hit_object->gaps(); # default = total (query + hit)
Returns : scalar context: integer
: array context without args: two-element list of integers
: (queryGaps, sbjctGaps)
: Array context can be forced by providing an argument of 'list' or 'array'.
:
: CAUTION: Calling this method within printf or sprintf is arrray context.
: So this function may not give you what you expect. For example:
: printf "Total gaps: %d", $hit->gaps();
: Actually returns a two-element array, so what gets printed
: is the number of gaps in the query, not the total
:
Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total' | 'list' (default = 'total')
('sbjct' is synonymous with 'hit')
Throws : n/a
Comments : If you need data for each HSP, use hsps() and then interate
: through each HSP object.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically..
: Not relying on wantarray since that will fail in situations
: such as printf "%d", $hit->gaps() in which you might expect to
: be printing the total gaps, but evaluates to array context.
See Also : length_aln()matches
Usage : $hit_object->matches( [class] );
Purpose : Get the total number of identical or conserved matches
: (or both) across all HSPs.
: (Note: 'conservative' matches are indicated as 'positives'
: in the Blast report.)
Example : ($id,$cons) = $hit_object->matches(); # no argument
: $id = $hit_object->matches('id');
: $cons = $hit_object->matches('cons');
Returns : Integer or a 2-element array of integers
Argument : class = 'id' | 'cons' OR none.
: If no argument is provided, both identical and conservative
: numbers are returned in a two element list.
: (Other terms can be used to refer to the conservative
: matches, e.g., 'positive'. All that is checked is whether or
: not the supplied string starts with 'id'. If not, the
: conservative matches are returned.)
Throws : Exception if the requested data cannot be obtained.
Comments : If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
: Does not rely on wantarray to return a list. Only checks for
: the presence of an argument (no arg = return list).
See Also : Bio::Search::HSP::BlastHSP::matches(), hsps()start
Usage : $sbjct->start( [seq_type] );
Purpose : Gets the start coordinate for the query, sbjct, or both sequences
: in the PsiBlastHit object. If there is more than one HSP, the lowest start
: value of all HSPs is returned.
Example : $qbeg = $sbjct->start('query');
: $sbeg = $sbjct->start('hit');
: ($qbeg, $sbeg) = $sbjct->start();
Returns : scalar context: integer
: array context without args: list of two integers (queryStart, sbjctStart)
: Array context can be "induced" by providing an argument of 'list' or 'array'.
Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default = 'query')
('sbjct' is synonymous with 'hit')
Throws : n/a
Comments : This method requires that all HSPs be tiled. If there is more than one
: HSP and they have not already been tiled, they will be tiled first automatically..
: Remember that the start and end coordinates of all HSPs are
: normalized so that start < end. Strand information can be
: obtained by calling $hit->strand().
See Also : end(), range(), strand(), "HSP Tiling and Ambiguous Alignments",
Bio::Search::HSP::BlastHSP::start
end
Usage : $sbjct->end( [seq_type] );
Purpose : Gets the end coordinate for the query, sbjct, or both sequences
: in the PsiBlastHit object. If there is more than one HSP, the largest end
: value of all HSPs is returned.
Example : $qend = $sbjct->end('query');
: $send = $sbjct->end('hit');
: ($qend, $send) = $sbjct->end();
Returns : scalar context: integer
: array context without args: list of two integers (queryEnd, sbjctEnd)
: Array context can be "induced" by providing an argument of 'list' or 'array'.
Argument : In scalar context: seq_type = 'query' or 'sbjct'
: (case insensitive). If not supplied, 'query' is used.
Throws : n/a
Comments : This method requires that all HSPs be tiled. If there is more than one
: HSP and they have not already been tiled, they will be tiled first automatically..
: Remember that the start and end coordinates of all HSPs are
: normalized so that start < end. Strand information can be
: obtained by calling $hit->strand().
See Also : start(), range(), strand(), "HSP Tiling and Ambiguous Alignments",
Bio::Search::HSP::BlastHSP::end
range
Usage : $sbjct->range( [seq_type] );
Purpose : Gets the (start, end) coordinates for the query or sbjct sequence
: in the HSP alignment.
Example : ($qbeg, $qend) = $sbjct->range('query');
: ($sbeg, $send) = $sbjct->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()frac_identical
Usage : $hit_object->frac_identical( [seq_type] );
Purpose : Get the overall fraction of identical positions across all HSPs.
: The number refers to only the aligned regions and does not
: account for unaligned regions in between the HSPs, if any.
Example : $frac_iden = $hit_object->frac_identical('query');
Returns : Float (2-decimal precision, e.g., 0.75).
Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total'
: default = 'query' (but see comments below).
: ('sbjct' is synonymous with 'hit')
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 with an argument of 'total',
: this method will report different values depending on the
: version of BLAST used. Total does NOT take into account HSP
: tiling, so it should not be used.
:
: To get the fraction identical among only the aligned residues,
: ignoring the gaps, call this method without an argument or
: with an argument of 'query' or 'hit'.
:
: If you need data for each HSP, use hsps() and then iterate
: through the HSP objects.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically.
See Also : frac_conserved(), frac_aligned_query(), matches(), Bio::Search::BlastUtils::tile_hsps()frac_conserved
Usage : $hit_object->frac_conserved( [seq_type] );
Purpose : Get the overall fraction of conserved positions across all HSPs.
: The number refers to only the aligned regions and does not
: account for unaligned regions in between the HSPs, if any.
Example : $frac_cons = $hit_object->frac_conserved('hit');
Returns : Float (2-decimal precision, e.g., 0.75).
Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total'
: default = 'query' (but see comments below).
: ('sbjct' is synonymous with 'hit')
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:
: "Positives = 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 with an argument of 'total',
: this method will report different values depending on the
: version of BLAST used. Total does NOT take into account HSP
: tiling, so it should not be used.
:
: To get the fraction conserved among only the aligned residues,
: ignoring the gaps, call this method without an argument or
: with an argument of 'query' or 'hit'.
:
: If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically.
See Also : frac_identical(), matches(), Bio::Search::BlastUtils::tile_hsps()frac_aligned_query
Usage : $hit_object->frac_aligned_query();
Purpose : Get the fraction of the query sequence which has been aligned
: across all HSPs (not including intervals between non-overlapping
: HSPs).
Example : $frac_alnq = $hit_object->frac_aligned_query();
Returns : Float (2-decimal precision, e.g., 0.75).
Argument : n/a
Throws : n/a
Comments : If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
: To compute the fraction aligned, the logical length of the query
: sequence is used, meaning that for [T]BLASTX reports, the
: full length of the query sequence is converted into amino acids
: by dividing by 3. This is necessary because of the way
: the lengths of aligned sequences are computed.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically.
See Also : frac_aligned_hit(), logical_length(), length_aln(), Bio::Search::BlastUtils::tile_hsps()frac_aligned_hit
Usage : $hit_object->frac_aligned_hit();
Purpose : Get the fraction of the hit (sbjct) sequence which has been aligned
: across all HSPs (not including intervals between non-overlapping
: HSPs).
Example : $frac_alnq = $hit_object->frac_aligned_hit();
Returns : Float (2-decimal precision, e.g., 0.75).
Argument : n/a
Throws : n/a
Comments : If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
: To compute the fraction aligned, the logical length of the sbjct
: sequence is used, meaning that for TBLAST[NX] reports, the
: full length of the sbjct sequence is converted into amino acids
: by dividing by 3. This is necessary because of the way
: the lengths of aligned sequences are computed.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically.
See Also : frac_aligned_query(), matches(), , logical_length(), length_aln(),
Bio::Search::BlastUtils::tile_hsps()frac_aligned_sbjct
Same as frac_aligned_hit()num_unaligned_sbjct
Same as num_unaligned_hit()num_unaligned_hit
Usage : $hit_object->num_unaligned_hit();
Purpose : Get the number of the unaligned residues in the hit sequence.
: Sums across all all HSPs.
Example : $num_unaln = $hit_object->num_unaligned_hit();
Returns : Integer
Argument : n/a
Throws : n/a
Comments : See notes regarding logical lengths in the comments for frac_aligned_hit().
: They apply here as well.
: If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically..
See Also : num_unaligned_query(), Bio::Search::BlastUtils::tile_hsps(), frac_aligned_hit()num_unaligned_query
Usage : $hit_object->num_unaligned_query();
Purpose : Get the number of the unaligned residues in the query sequence.
: Sums across all all HSPs.
Example : $num_unaln = $hit_object->num_unaligned_query();
Returns : Integer
Argument : n/a
Throws : n/a
Comments : See notes regarding logical lengths in the comments for frac_aligned_query().
: They apply here as well.
: If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically..
See Also : num_unaligned_hit(), frac_aligned_query(), Bio::Search::BlastUtils::tile_hsps()seq_inds
Usage : $hit->seq_inds( seq_type, class, collapse );
Purpose : Get a list of residue positions (indices) across all HSPs
: for identical or conserved residues in the query or sbjct sequence.
Example : @s_ind = $hit->seq_inds('query', 'identical');
: @h_ind = $hit->seq_inds('hit', 'conserved');
: @h_ind = $hit->seq_inds('hit', 'conserved', 1);
Returns : Array of integers
: May include ranges if collapse is non-zero.
Argument : [0] seq_type = 'query' or 'hit' or 'sbjct' (default = 'query')
: ('sbjct' is synonymous with 'hit')
: [1] class = 'identical' or 'conserved' (default = 'identical')
: (can be shortened to 'id' or 'cons')
: (actually, anything not 'id' will evaluate to 'conserved').
: [2] collapse = boolean, if non-zero, 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 : Note that HSPs are not tiled for this. This could be a problem
: for hits containing mutually exclusive HSPs.
: TODO: Consider tiling and then reporting seq_inds for the
: best HSP contig.
See Also : Bio::Search::HSP::BlastHSP::seq_inds()iteration
Usage : $sbjct->iteration( );
Purpose : Gets the iteration number in which the Hit was found.
Example : $iteration_num = $sbjct->iteration();
Returns : Integer greater than or equal to 1
Non-PSI-BLAST reports will report iteration as 1, but this number
is only meaningful for PSI-BLAST reports.
Argument : none
Throws : none
See Also : found_again()found_again
Usage : $sbjct->found_again;
Purpose : Gets a boolean indicator whether or not the hit has
been found in a previous iteration.
This is only applicable to PSI-BLAST reports.
This method indicates if the hit was reported in the
"Sequences used in model and found again" section of the
PSI-BLAST report or if it was reported in the
"Sequences not found previously or not previously below threshold"
section of the PSI-BLAST report. Only for hits in iteration > 1.
Example : if( $sbjct->found_again()) { ... };
Returns : Boolean (1 or 0) for PSI-BLAST report iterations greater than 1.
Returns undef for PSI-BLAST report iteration 1 and non PSI_BLAST
reports.
Argument : none
Throws : none
See Also : found_again()strand
Usage : $sbjct->strand( [seq_type] );
Purpose : Gets the strand(s) for the query, sbjct, or both sequences
: in the best HSP of the PsiBlastHit object after HSP tiling.
: Only valid for BLASTN, TBLASTX, BLASTX-query, TBLASTN-hit.
Example : $qstrand = $sbjct->strand('query');
: $sstrand = $sbjct->strand('hit');
: ($qstrand, $sstrand) = $sbjct->strand();
Returns : scalar context: integer '1', '-1', or '0'
: array context without args: list of two strings (queryStrand, sbjctStrand)
: Array context can be "induced" by providing an argument of 'list' or 'array'.
Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default = 'query')
('sbjct' is synonymous with 'hit')
Throws : n/a
Comments : This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically..
: If you don't want the tiled data, iterate through each HSP
: calling strand() on each (use hsps() to get all HSPs).
:
: Formerly (prior to 10/21/02), this method would return the
: string "-1/1" for hits with HSPs on both strands.
: However, now that strand and frame is properly being accounted
: for during HSP tiling, it makes more sense for strand()
: to return the strand data for the best HSP after tiling.
:
: If you really want to know about hits on opposite strands,
: you should be iterating through the HSPs using methods on the
: HSP objects.
:
: A possible use case where knowing whether a hit has HSPs
: on both strands would be when filtering via SearchIO for hits with
: this property. However, in this case it would be better to have a
: dedicated method such as $hit->hsps_on_both_strands(). Similarly
: for frame. This could be provided if there is interest.
See Also : Bio::Search::HSP::BlastHSP::strand()
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