Bio::Search::HSP PsiBlastHSP
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Summary
Bio::Search::HSP::PsiBlastHSP - Bioperl BLAST High-Scoring Pair object
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::Similarity
Inherit
Bio::Search::HSP::HSPI Bio::SeqFeature::SimilarityPair
Synopsis
See Bio::Search::Hit::BlastHit.
Description
A Bio::Search::HSP::PsiBlastHSP object provides an interface to data
obtained in a single alignment section of a Blast report (known as a
"High-scoring Segment Pair"). This is essentially a pairwise
alignment with score information.
PsiBlastHSP objects are accessed via Bio::Search::Hit::BlastHit
objects after parsing a BLAST report using the Bio::SearchIO
system.
The construction of PsiBlastHSP objects is performed by
Bio::Factory::BlastHitFactory in a process that is
orchestrated by the Blast parser (Bio::SearchIO::psiblast).
The resulting PsiBlastHSPs are then accessed via
Bio::Search::Hit::BlastHit). Therefore, you do not need to
use Bio::Search::HSP::PsiBlastHSP) directly. If you need to construct
PsiBlastHSPs directly, see the new() function for details.
For Bio::SearchIO BLAST parsing usage examples, see the
examples/search-blast directory of the Bioperl distribution. Sequence endpoints are swapped so that start is always less than
end. This affects For TBLASTN/X hits on the minus strand. Strand
information can be recovered using the strand() method. This
normalization step is standard Bioperl practice. It also facilitates
use of range information by methods such as match().
 * 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.
Methods
newDescriptionCode
_id_str
No description
Code
algorithmDescriptionCode
signifDescriptionCode
evalueDescriptionCode
pDescriptionCode
pvalue
No description
Code
lengthDescriptionCode
gapsDescriptionCode
frac_identicalDescriptionCode
frac_conservedDescriptionCode
query_stringDescriptionCode
hit_stringDescriptionCode
homology_stringDescriptionCode
expectDescriptionCode
rankDescriptionCode
name
No description
Code
to_stringDescriptionCode
_set_dataDescriptionCode
_set_score_statsDescriptionCode
_set_match_statsDescriptionCode
_set_seq_dataDescriptionCode
_set_seqDescriptionCode
_set_residuesDescriptionCode
_set_match_seqDescriptionCode
nDescriptionCode
matchesDescriptionCode
num_identicalDescriptionCode
num_conservedDescriptionCode
rangeDescriptionCode
startDescriptionCode
endDescriptionCode
strandDescriptionCode
seqDescriptionCode
seq_strDescriptionCode
seq_indsDescriptionCode
get_alnDescriptionCode
Methods description
newcode    nextTop
 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 : Bio::SeqFeature::SimilarityPair::new(), Bio::SeqFeature::Similarity::new()
algorithmcodeprevnextTop
 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()codeprevnextTop
 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()
evaluecodeprevnextTop
 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
pcodeprevnextTop
 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
lengthcodeprevnextTop
 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
gapscodeprevnextTop
 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_identicalcodeprevnextTop
 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_conservedcodeprevnextTop
 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_stringcodeprevnextTop
 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_stringcodeprevnextTop
 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_stringcodeprevnextTop
 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
expectcodeprevnextTop
See Bio::Search::HSP::HSPI::expect()
rankcodeprevnextTop
 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_stringcodeprevnextTop
 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_datacodeprevnextTop
 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_statscodeprevnextTop
 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_statscodeprevnextTop
 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_datacodeprevnextTop
 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_seqcodeprevnextTop
 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_residuescodeprevnextTop
 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_seqcodeprevnextTop
 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
ncodeprevnextTop
 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()
matchescodeprevnextTop
 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_identicalcodeprevnextTop
 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_conservedcodeprevnextTop
 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
rangecodeprevnextTop
 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
startcodeprevnextTop
 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
endcodeprevnextTop
 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
strandcodeprevnextTop
 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
seqcodeprevnextTop
 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_strcodeprevnextTop
 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_indscodeprevnextTop
 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_alncodeprevnextTop
 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 $GAP_SYMBOL).
See Also : /seq, Bio::SimpleAlign
Methods code
newdescriptionprevnextTop
sub new {
#----------------
my ($class, @args ) = @_; my $self = $class->SUPER::new( @args ); # Initialize placeholders
$self->{'_queryGaps'} = $self->{'_sbjctGaps'} = 0; my ($raw_data, $qname, $hname, $qlen, $hlen); ($self->{'_prog'}, $self->{'_rank'}, $raw_data, $qname, $hname) = $self->_rearrange([qw( PROGRAM RANK RAW_DATA QUERY_NAME HIT_NAME )], @args ); # _set_data() does a fair amount of parsing.
# This will likely change (see comment above.)
$self->_set_data( @{$raw_data} ); # Store the aligned query as sequence feature
my ($qb, $hb) = ($self->start()); my ($qe, $he) = ($self->end()); my ($qs, $hs) = ($self->strand()); my ($qf,$hf) = ($self->query->frame(), $self->hit->frame); $self->query( Bio::SeqFeature::Similarity->new (-start =>$qb, -end =>$qe, -strand =>$qs, -bits =>$self->bits, -score =>$self->score, -frame =>$qf, -seq_id => $qname, -source =>$self->{'_prog'} )); $self->hit( Bio::SeqFeature::Similarity->new (-start =>$hb, -end =>$he, -strand =>$hs, -bits =>$self->bits, -score =>$self->score, -frame =>$hf, -seq_id => $hname, -source =>$self->{'_prog'} )); # set lengths
$self->query->seqlength($qlen); # query
$self->hit->seqlength($hlen); # subject
$self->query->frac_identical($self->frac_identical('query')); $self->hit->frac_identical($self->frac_identical('hit')); return $self; } #sub DESTROY {
# my $self = shift;
# #print STDERR "--->DESTROYING $self\n";
#}
# Title : _id_str;
# Purpose : Intended for internal use only to provide a string for use
# within exception messages to help users figure out which
# query/hit caused the problem.
# Returns : Short string with name of query and hit seq
}
_id_strdescriptionprevnextTop
sub _id_str {
    my $self = shift;
    if( not defined $self->{'_id_str'}) {
        my $qname = $self->query->seqname;
        my $hname = $self->hit->seqname;
        $self->{'_id_str'} = "QUERY=\"$qname\" HIT=\"$hname\"";
    }
    return $self->{'_id_str'};
}

#=================================================
# Begin Bio::Search::HSP::HSPI implementation
#=================================================
}
algorithmdescriptionprevnextTop
sub algorithm {
#----------------
my ($self,@args) = @_; return $self->{'_prog'};
}
signifdescriptionprevnextTop
sub signif {
#-----------
my $self = shift; my $val ||= defined($self->{'_p'}) ? $self->{'_p'} : $self->{'_expect'}; $val;
}
evaluedescriptionprevnextTop
sub evalue {
 shift->{'_expect'}
}
pdescriptionprevnextTop
sub p {
 my $self = shift; $self->{'_p'};
}
pvaluedescriptionprevnextTop
sub pvalue {
 shift->p(@_);
}
lengthdescriptionprevnextTop
sub length {
#-----------
## Developer note: when using the built-in length function within
## this module, call it as CORE::length().
my( $self, $seqType ) = @_; $seqType ||= 'total'; $seqType = 'sbjct' if $seqType eq 'hit'; $seqType ne 'total' and $self->_set_seq_data() unless $self->{'_set_seq_data'}; ## Sensitive to member name format.
$seqType = "_\L$seqType\E"; $self->{$seqType.'Length'};
}
gapsdescriptionprevnextTop
sub gaps {
#---------
my( $self, $seqType ) = @_; $self->_set_seq_data() unless $self->{'_set_seq_data'}; $seqType ||= (wantarray ? 'list' : 'total'); $seqType = 'sbjct' if $seqType eq 'hit'; if($seqType =~ /list|array/i) { return (($self->{'_queryGaps'} || 0), ($self->{'_sbjctGaps'} || 0)); } if($seqType eq 'total') { return ($self->{'_queryGaps'} + $self->{'_sbjctGaps'}) || 0; } else { ## Sensitive to member name format.
$seqType = "_\L$seqType\E"; return $self->{$seqType.'Gaps'} || 0; }
}
frac_identicaldescriptionprevnextTop
sub frac_identical {
#-------------------
# The value is calculated as opposed to storing it from the parsed results.
# This saves storage and also permits flexibility in determining for which
# sequence (query or sbjct) the figure is to be calculated.
my( $self, $seqType ) = @_; $seqType ||= 'total'; $seqType = 'sbjct' if $seqType eq 'hit'; if($seqType ne 'total') { $self->_set_seq_data() unless $self->{'_set_seq_data'}; } ## Sensitive to member name format.
$seqType = "_\L$seqType\E"; sprintf( "%.2f", $self->{'_numIdentical'}/$self->{$seqType.'Length'});
}
frac_conserveddescriptionprevnextTop
sub frac_conserved {
#--------------------
# The value is calculated as opposed to storing it from the parsed results.
# This saves storage and also permits flexibility in determining for which
# sequence (query or sbjct) the figure is to be calculated.
my( $self, $seqType ) = @_; $seqType ||= 'total'; $seqType = 'sbjct' if $seqType eq 'hit'; if($seqType ne 'total') { $self->_set_seq_data() unless $self->{'_set_seq_data'}; } ## Sensitive to member name format.
$seqType = "_\L$seqType\E"; sprintf( "%.2f", $self->{'_numConserved'}/$self->{$seqType.'Length'});
}
query_stringdescriptionprevnextTop
sub query_string {
shift->seq_str('query');
}
hit_stringdescriptionprevnextTop
sub hit_string {
shift->seq_str('hit');
}
homology_stringdescriptionprevnextTop
sub homology_string {
shift->seq_str('match');
}
expectdescriptionprevnextTop
sub expect {
 shift->evalue( @_ );
}
rankdescriptionprevnextTop
sub rank {
 shift->{'_rank'}
}
namedescriptionprevnextTop
sub name {
 shift->rank
}
to_stringdescriptionprevnextTop
sub to_string {
#----------
my $self = shift; return "[PsiBlastHSP] " . $self->rank();
}
_set_datadescriptionprevnextTop
sub _set_data {
#--------------
my $self = shift; my @data = @_; my @queryList = (); # 'Query' = SEQUENCE USED TO QUERY THE DATABASE.
my @sbjctList = (); # 'Sbjct' = HOMOLOGOUS SEQUENCE FOUND IN THE DATABASE.
my @matchList = (); my $matchLine = 0; # Alternating boolean: when true, load 'match' data.
my @linedat = (); #print STDERR "PsiBlastHSP: set_data()\n";
my($line, $aln_row_len, $length_diff); $length_diff = 0; # Collecting data for all lines in the alignment
# and then storing the collections for possible processing later.
#
# Note that "match" lines may not be properly padded with spaces.
# This loop now properly handles such cases:
# Query: 1141 PSLVELTIRDCPRLEVGPMIRSLPKFPMLKKLDLAVANIIEEDLDVIGSLEELVIXXXXX 1200
# PSLVELTIRDCPRLEVGPMIRSLPKFPMLKKLDLAVANIIEEDLDVIGSLEELVI
# Sbjct: 1141 PSLVELTIRDCPRLEVGPMIRSLPKFPMLKKLDLAVANIIEEDLDVIGSLEELVILSLKL 1200
foreach $line( @data ) { next if $line =~ /^\s*$/; if( $line =~ /^ ?Score/ ) { $self->_set_score_stats( $line ); } elsif( $line =~ /^ ?(Identities|Positives|Strand)/ ) { $self->_set_match_stats( $line ); } elsif( $line =~ /^ ?Frame = ([\d+-]+)/ ) { # Version 2.0.8 has Frame information on a separate line.
# Storing frame according to SeqFeature::Generic::frame()
# which does not contain strand info (use strand()).
my $frame = abs($1) - 1; $self->frame( $frame ); } elsif( $line =~ /^(Query:?[\s\d]+)([^\s\d]+)/ ) { push @queryList, $line; $self->{'_match_indent'} = CORE::length $1; $aln_row_len = (CORE::length $1) + (CORE::length $2); $matchLine = 1; } elsif( $matchLine ) { # Pad the match line with spaces if necessary.
$length_diff = $aln_row_len - CORE::length $line; $length_diff and $line .= ' 'x $length_diff; push @matchList, $line; $matchLine = 0; } elsif( $line =~ /^Sbjct/ ) { push @sbjctList, $line; } } # Storing the query and sbjct lists in case they are needed later.
# We could make this conditional to save memory.
$self->{'_queryList'} =\@ queryList; $self->{'_sbjctList'} =\@ sbjctList; # Storing the match list in case it is needed later.
$self->{'_matchList'} =\@ matchList; if(not defined ($self->{'_numIdentical'})) { my $id_str = $self->_id_str; $self->throw( -text => "Can't parse match statistics. Possibly a new or unrecognized Blast format. ($id_str)"); } if(!scalar @queryList or !scalar @sbjctList) { my $id_str = $self->_id_str; $self->throw( "Can't find query or sbjct alignment lines. Possibly unrecognized Blast format. ($id_str)"); }
}
_set_score_statsdescriptionprevnextTop
sub _set_score_stats {
#--------------------
my ($self, $data) = @_; my ($expect, $p); if($data =~ /Score = +([\d.e+-]+) bits \(([\d.e+-]+)\), +Expect = +([\d.e+-]+)/) { # blast2 format n = 1
$self->bits($1); $self->score($2); $expect = $3; } elsif($data =~ /Score = +([\d.e+-]+) bits \(([\d.e+-]+)\), +Expect\((\d+)\) = +([\d.e+-]+)/) { # blast2 format n > 1
$self->bits($1); $self->score($2); $self->{'_n'} = $3; $expect = $4; } elsif($data =~ /Score = +([\d.e+-]+) \(([\d.e+-]+) bits\), +Expect = +([\d.e+-]+), P = +([\d.e-]+)/) { # blast1 format, n = 1
$self->score($1); $self->bits($2); $expect = $3; $p = $4; } elsif($data =~ /Score = +([\d.e+-]+) \(([\d.e+-]+) bits\), +Expect = +([\d.e+-]+), +Sum P\((\d+)\) = +([\d.e-]+)/) { # blast1 format, n > 1
$self->score($1); $self->bits($2); $expect = $3; $self->{'_n'} = $4; $p = $5; } else { my $id_str = $self->_id_str; $self->throw(-class => 'Bio::Root::Exception', -text => "Can't parse score statistics: unrecognized format. ($id_str)", -value => $data); } $expect = "1$expect" if $expect =~ /^e/i; $p = "1$p" if defined $p and $p=~ /^e/i; $self->{'_expect'} = $expect; $self->{'_p'} = $p || undef; $self->significance( $p || $expect );
}
_set_match_statsdescriptionprevnextTop
sub _set_match_stats {
#--------------------
my ($self, $data) = @_; if($data =~ m!Identities = (\d+)/(\d+)!) {
# blast1 or 2 format
$self->{'_numIdentical'} = $1;
$self->{'_totalLength'} = $2; } if($data =~ m!Positives = (\d+)/(\d+)!) {
# blast1 or 2 format
$self->{'_numConserved'} = $1;
$self->{'_totalLength'} = $2; } if($data =~ m!Frame = ([\d+-]+)!) {
$self->frame($1);
} # Strand data is not always present in this line.
# _set_seq() will also set strand information.
if($data =~ m!Strand = (\w+) / (\w+)!) {
$self->{'_queryStrand'} = $1;
$self->{'_sbjctStrand'} = $2; } # if($data =~ m!Gaps = (\d+)/(\d+)!) {
# $self->{'_totalGaps'} = $1;
# } else {
# $self->{'_totalGaps'} = 0;
# }
}
_set_seq_datadescriptionprevnextTop
sub _set_seq_data {
#-----------------
my $self = shift; $self->_set_seq('query', @{$self->{'_queryList'}}); $self->_set_seq('sbjct', @{$self->{'_sbjctList'}}); # Liberate some memory.
@{$self->{'_queryList'}} = @{$self->{'_sbjctList'}} = (); undef $self->{'_queryList'}; undef $self->{'_sbjctList'}; $self->{'_set_seq_data'} = 1;
}
_set_seqdescriptionprevnextTop
sub _set_seq {
#-------------
my $self = shift; my $seqType = shift; my @data = @_; my @ranges = (); my @sequence = (); my $numGaps = 0; foreach( @data ) { if( m/(\d+) *([^\d\s]+) *(\d+)/) {
push
@ranges, ( $1, $3 ) ;
push @sequence, $2; #print STDERR "_set_seq found sequence \"$2\"\n";
} else { $self->warn("Bad sequence data: $_"); } } if( !(scalar(@sequence) and scalar(@ranges))) { my $id_str = $self->_id_str; $self->throw("Can't set sequence: missing data. Possibly unrecognized Blast format. ($id_str)"); } # Sensitive to member name changes.
$seqType = "_\L$seqType\E"; $self->{$seqType.'Start'} = $ranges[0]; $self->{$seqType.'Stop'} = $ranges[ $#ranges ]; $self->{$seqType.'Seq'} =\@ sequence; $self->{$seqType.'Length'} = abs($ranges[ $#ranges ] - $ranges[0]) + 1; # Adjust lengths for BLASTX, TBLASTN, TBLASTX sequences
# Converting nucl coords to amino acid coords.
my $prog = $self->algorithm; if($prog eq 'TBLASTN' and $seqType eq '_sbjct') { $self->{$seqType.'Length'} /= 3;
} elsif($prog eq 'BLASTX' and $seqType eq '_query') { $self->{$seqType.'Length'} /= 3;
} elsif($prog eq 'TBLASTX') { $self->{$seqType.'Length'} /= 3;
} if( $prog ne 'BLASTP' ) { $self->{$seqType.'Strand'} = 'Plus' if $prog =~ /BLASTN/; $self->{$seqType.'Strand'} = 'Plus' if ($prog =~ /BLASTX/ and $seqType eq '_query'); # Normalize sequence endpoints so that start < end.
# Reverse complement or 'minus strand' HSPs get flipped here.
if($self->{$seqType.'Start'} > $self->{$seqType.'Stop'}) { ($self->{$seqType.'Start'}, $self->{$seqType.'Stop'}) = ($self->{$seqType.'Stop'}, $self->{$seqType.'Start'}); $self->{$seqType.'Strand'} = 'Minus'; } } ## Count number of gaps in each seq. Only need to do this for gapped Blasts.
# if($self->{'_gapped'}) {
my $seqstr = join('', @sequence); $seqstr =~ s/\s//g; my $num_gaps = CORE::length($seqstr) - $self->{$seqType.'Length'}; $self->{$seqType.'Gaps'} = $num_gaps if $num_gaps > 0; # }
}
_set_residuesdescriptionprevnextTop
sub _set_residues {
#------------------
my $self = shift; my @sequence = (); $self->_set_seq_data() unless $self->{'_set_seq_data'}; # Using hashes to avoid saving duplicate residue numbers.
my %identicalList_query = (); my %identicalList_sbjct = (); my %conservedList_query = (); my %conservedList_sbjct = (); my $aref = $self->_set_match_seq() if not ref $self->{'_matchSeq'}; $aref ||= $self->{'_matchSeq'}; my $seqString = join('', @$aref ); my $qseq = join('',@{$self->{'_querySeq'}}); my $sseq = join('',@{$self->{'_sbjctSeq'}}); my $resCount_query = $self->{'_queryStop'} || 0; my $resCount_sbjct = $self->{'_sbjctStop'} || 0; my $prog = $self->algorithm; if($prog !~ /^BLASTP|^BLASTN/) { if($prog eq 'TBLASTN') { $resCount_sbjct /= 3;
} elsif($prog eq 'BLASTX') { $resCount_query /= 3;
} elsif($prog eq 'TBLASTX') { $resCount_query /= 3;
$resCount_sbjct /= 3;
} } my ($mchar, $schar, $qchar); while( $mchar = chop($seqString) ) { ($qchar, $schar) = (chop($qseq), chop($sseq)); if( $mchar eq '+' ) { $conservedList_query{ $resCount_query } = 1; $conservedList_sbjct{ $resCount_sbjct } = 1; } elsif( $mchar ne ' ' ) { $identicalList_query{ $resCount_query } = 1; $identicalList_sbjct{ $resCount_sbjct } = 1; } $resCount_query-- if $qchar ne $GAP_SYMBOL; $resCount_sbjct-- if $schar ne $GAP_SYMBOL; } $self->{'_identicalRes_query'} =\% identicalList_query; $self->{'_conservedRes_query'} =\% conservedList_query; $self->{'_identicalRes_sbjct'} =\% identicalList_sbjct; $self->{'_conservedRes_sbjct'} =\% conservedList_sbjct;
}
_set_match_seqdescriptionprevnextTop
sub _set_match_seq {
#-------------------
my $self = shift; if( ! ref($self->{'_matchList'}) ) { my $id_str = $self->_id_str; $self->throw("Can't set HSP match sequence: No data ($id_str)"); } my @data = @{$self->{'_matchList'}}; my(@sequence); foreach( @data ) { chomp($_); ## Remove leading spaces; (note: aln may begin with a space
## which is why we can't use s/^ +//).
s/^ {$self->{'_match_indent'}}//; push @sequence, $_; } # Liberate some memory.
@{$self->{'_matchList'}} = undef; $self->{'_matchList'} = undef; $self->{'_matchSeq'} =\@ sequence; return $self->{'_matchSeq'};
}
ndescriptionprevnextTop
sub n {
 my $self = shift; $self->{'_n'} || '';
}
matchesdescriptionprevnextTop
sub matches {
#-----------
my( $self, %param ) = @_; my(@data); my($seqType, $beg, $end) = ($param{-SEQ}, $param{-START}, $param{-STOP}); $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; my($start,$stop); if(!defined $beg && !defined $end) { ## Get data for the whole alignment.
push @data, ($self->{'_numIdentical'}, $self->{'_numConserved'}); } else { ## Get the substring representing the desired sub-section of aln.
$beg ||= 0; $end ||= 0; ($start,$stop) = $self->range($seqType); if($beg == 0) { $beg = $start; $end = $beg+$end; } elsif($end == 0) { $end = $stop; $beg = $end-$beg; } if($end >= $stop) { $end = $stop; } ##ML changed from if (end >stop)
else { $end += 1;} ##ML moved from commented position below, makes
##more sense here
# if($end > $stop) { $end = $stop; }
if($beg < $start) { $beg = $start; } # else { $end += 1;}
# my $seq = substr($self->seq_str('match'), $beg-$start, ($end-$beg));
## ML: START fix for substr out of range error ------------------
my $seq = ""; my $prog = $self->algorithm; if (($prog eq 'TBLASTN') and ($seqType eq 'sbjct')) { $seq = substr($self->seq_str('match'), int(($beg-$start)/3), int(($end-$beg+1)/3)); } elsif (($prog eq 'BLASTX') and ($seqType eq 'query')) { $seq = substr($self->seq_str('match'), int(($beg-$start)/3), int(($end-$beg+1)/3)); } else { $seq = substr($self->seq_str('match'), $beg-$start, ($end-$beg)); } ## ML: End of fix for substr out of range error -----------------
## ML: debugging code
## This is where we get our exception. Try printing out the values going
## into this:
##
# print STDERR
# qq(*------------MY EXCEPTION --------------------\nSeq: ") ,
# $self->seq_str("$seqType"), qq("\n),$self->rank,",( index:";
# print STDERR $beg-$start, ", len: ", $end-$beg," ), (HSPRealLen:",
# CORE::length $self->seq_str("$seqType");
# print STDERR ", HSPCalcLen: ", $stop - $start +1 ," ),
# ( beg: $beg, end: $end ), ( start: $start, stop: stop )\n";
## ML: END DEBUGGING CODE----------
if(!CORE::length $seq) { my $id_str = $self->_id_str; $self->throw("Undefined $seqType sub-sequence ($beg,$end). Valid range = $start - $stop ($id_str)"); } ## Get data for a substring.
# printf "Collecting HSP subsection data: beg,end = %d,%d; start,stop = %d,%d\n%s<---\n", $beg, $end, $start, $stop, $seq;
# printf "Original match seq:\n%s\n",$self->seq_str('match');
$seq =~ s/ //g; # remove space (no info).
my $len_cons = CORE::length $seq; $seq =~ s/\+//g; # remove '+' characters (conservative substitutions)
my $len_id = CORE::length $seq; push @data, ($len_id, $len_cons); # printf " HSP = %s\n id = %d; cons = %d\n", $self->rank, $len_id, $len_cons; <STDIN>;
} @data;
}
num_identicaldescriptionprevnextTop
sub num_identical {
#-------------------
my( $self) = shift; $self->{'_numIdentical'};
}
num_conserveddescriptionprevnextTop
sub num_conserved {
#-------------------
my( $self) = shift; $self->{'_numConserved'};
}
rangedescriptionprevnextTop
sub range {
#----------
my ($self, $seqType) = @_; $self->_set_seq_data() unless $self->{'_set_seq_data'}; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; ## Sensitive to member name changes.
$seqType = "_\L$seqType\E"; return ($self->{$seqType.'Start'},$self->{$seqType.'Stop'});
}
startdescriptionprevnextTop
sub start {
#----------
my ($self, $seqType) = @_; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; $self->_set_seq_data() unless $self->{'_set_seq_data'}; if($seqType =~ /list|array/i) { return ($self->{'_queryStart'}, $self->{'_sbjctStart'}); } else { ## Sensitive to member name changes.
$seqType = "_\L$seqType\E"; return $self->{$seqType.'Start'}; }
}
enddescriptionprevnextTop
sub end {
#----------
my ($self, $seqType) = @_; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; $self->_set_seq_data() unless $self->{'_set_seq_data'}; if($seqType =~ /list|array/i) { return ($self->{'_queryStop'}, $self->{'_sbjctStop'}); } else { ## Sensitive to member name changes.
$seqType = "_\L$seqType\E"; return $self->{$seqType.'Stop'}; }
}
stranddescriptionprevnextTop
sub strand {
#-----------
my( $self, $seqType ) = @_; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; ## Sensitive to member name format.
$seqType = "_\L$seqType\E"; # $seqType could be '_list'.
$self->{'_queryStrand'} or $self->_set_seq_data() unless $self->{'_set_seq_data'}; my $prog = $self->algorithm; if($seqType =~ /list|array/i) { my ($qstr, $hstr); if( $prog eq 'BLASTP') { $qstr = 0; $hstr = 0; } elsif( $prog eq 'TBLASTN') { $qstr = 0; $hstr = $STRAND_SYMBOL{$self->{'_sbjctStrand'}}; } elsif( $prog eq 'BLASTX') { $qstr = $STRAND_SYMBOL{$self->{'_queryStrand'}}; $hstr = 0; } else { $qstr = $STRAND_SYMBOL{$self->{'_queryStrand'}} if defined $self->{'_queryStrand'}; $hstr = $STRAND_SYMBOL{$self->{'_sbjctStrand'}} if defined $self->{'_sbjctStrand'}; } $qstr ||= 0; $hstr ||= 0; return ($qstr, $hstr); } local $^W = 0; $STRAND_SYMBOL{$self->{$seqType.'Strand'}} || 0;
}
seqdescriptionprevnextTop
sub seq {
#-------
my($self,$seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; my $str = $self->seq_str($seqType); require Bio::Seq; Bio::Seq->new(-ID => $self->to_string, -SEQ => $str, -DESC => "$seqType sequence", );
}
seq_strdescriptionprevnextTop
sub seq_str {
#------------
my($self,$seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; ## Sensitive to member name changes.
$seqType = "_\L$seqType\E"; $self->_set_seq_data() unless $self->{'_set_seq_data'}; if($seqType =~ /sbjct|query/) { my $seq = join('',@{$self->{$seqType.'Seq'}}); $seq =~ s/\s+//g; return $seq; } elsif( $seqType =~ /match/i) { # Only need to call _set_match_seq() if the match seq is requested.
my $aref = $self->_set_match_seq() unless ref $self->{'_matchSeq'}; $aref = $self->{'_matchSeq'}; return join('',@$aref); } else { my $id_str = $self->_id_str; $self->throw(-class => 'Bio::Root::BadParameter', -text => "Invalid or undefined sequence type: $seqType ($id_str)\n" . "Valid types: query, sbjct, match", -value => $seqType); }
}
seq_indsdescriptionprevnextTop
sub seq_inds {
#---------------
my ($self, $seqType, $class, $collapse) = @_; $seqType ||= 'query'; $class ||= 'identical'; $collapse ||= 0; $seqType = 'sbjct' if $seqType eq 'hit'; $self->_set_residues() unless defined $self->{'_identicalRes_query'}; $seqType = ($seqType !~ /^q/i ? 'sbjct' : 'query'); $class = ($class !~ /^id/i ? 'conserved' : 'identical'); ## Sensitive to member name changes.
$seqType = "_\L$seqType\E"; $class = "_\L$class\E"; my @ary = sort { $a <=> $b } keys %{ $self->{"${class}Res$seqType"}}; require Bio::Search::BlastUtils if $collapse; return $collapse ? &Bio::Search::BlastUtils::collapse_nums(@ary) : @ary;
}
get_alndescriptionprevnextTop
sub get_aln {
#------------
my $self = shift; require Bio::SimpleAlign; require Bio::LocatableSeq; my $qseq = $self->seq('query'); my $sseq = $self->seq('sbjct'); my $type = $self->algorithm =~ /P$|^T/ ? 'amino' : 'dna'; my $aln = Bio::SimpleAlign->new(); $aln->add_seq(Bio::LocatableSeq->new(-seq => $qseq->seq(), -id => 'query_'.$qseq->display_id(), -start => 1, -end => CORE::length($qseq))); $aln->add_seq(Bio::LocatableSeq->new(-seq => $sseq->seq(), -id => 'hit_'.$sseq->display_id(), -start => 1, -end => CORE::length($sseq))); return $aln; } 1; __END__
}
General documentation
DEPENDENCIESTop
Bio::Search::HSP::PsiBlastHSP.pm is a concrete class that inherits from
Bio::SeqFeature::SimilarityPair and Bio::Search::HSP::HSPI.
Bio::Seq and Bio::SimpleAlign are employed for creating
sequence and alignment objects, respectively.
Relationship to L<Bio::SimpleAlign> and Bio::SeqTop
PsiBlastHSP.pm can provide the query or sbjct sequence as a Bio::Seq
object via the seq() method. The PsiBlastHSP.pm object can also create a
two-sequence Bio::SimpleAlign alignment object using the the query
and sbjct sequences via the get_aln() method. Creation of alignment
objects is not automatic when constructing the PsiBlastHSP.pm object since
this level of functionality is not always required and would generate
a lot of extra overhead when crunching many reports.
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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 BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Steve Chervitz <sac-at-bioperl.org>
See the FEEDBACK section for where to send bug reports and comments.
ACKNOWLEDGEMENTSTop
This software was originally developed in the Department of Genetics
at Stanford University. I would also like to acknowledge my
colleagues at Affymetrix for useful feedback.
SEE ALSOTop
 Bio::Search::Hit::BlastHit.pm          - Blast hit object.
Bio::Search::Result::BlastResult.pm - Blast Result object.
Bio::Seq.pm - Biosequence object
Links:Top
 http://bio.perl.org/                       - Bioperl Project Homepage
COPYRIGHTTop
Copyright (c) 1996-2001 Steve Chervitz. All Rights Reserved.
DISCLAIMERTop
This software is provided "as is" without warranty of any kind.
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
FOR DEVELOPERS ONLYTop
Data MembersTop
Information about the various data members of this module is provided for those
wishing to modify or understand the code. Two things to bear in mind:
    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 ^^^^^^^^^^^^^