Bio::Search::Hit ModelHit
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Summary
Bio::Search::Hit::ModelHit - A model-based implementation of the Bio::Search::Hit::HitI interface
Package variables
No package variables defined.
Inherit
Bio::Search::Hit::GenericHit
Synopsis
    use Bio::Search::Hit::ModelHit;
my $hit = Bio::Search::Hit::ModelHit->new(-algorithm => 'rnamotif');
# typically one gets HitI objects from a SearchIO stream via a ResultI use Bio::SearchIO; my $parser = Bio::SearchIO->new(-format => 'infernal', -file => 'trap.inf'); my $result = $parser->next_result; my $hit = $result->next_hit;
Description
This object handles the hit data from a database search using models or
descriptors instead of sequences, such as Infernal, HMMER, RNAMotif, etc.
Unless you're writing a parser, you won't ever need to create a ModelHit or
any other HitI-implementing object. If you use the SearchIO system, HitI objects
are created automatically from a SearchIO stream which returns
Bio::Search::Hit::HitI objects.
Note that several HitI-based methods have been overridden from ModelHit due to
their unreliability when dealing with queries that aren't sequence-based. It may
be possible to reimplement these at a later point, but for the time being they
will throw warnings and return w/o results.
For documentation on what you can do with ModelHit (and other HitI objects),
please see the API documentation in
Bio::Search::Hit::HitI.
Methods
overlapDescriptionCode
nDescriptionCode
hspDescriptionCode
rankDescriptionCode
locusDescriptionCode
each_accession_numberDescriptionCode
query_lengthDescriptionCode
ncbi_giDescriptionCode
length_alnDescriptionCode
gapsDescriptionCode
matchesDescriptionCode
startDescriptionCode
endDescriptionCode
rangeDescriptionCode
frac_identicalDescriptionCode
frac_conservedDescriptionCode
frac_aligned_queryDescriptionCode
frac_aligned_hitDescriptionCode
num_unaligned_hitDescriptionCode
num_unaligned_queryDescriptionCode
seq_indsDescriptionCode
strandDescriptionCode
frameDescriptionCode
logical_lengthDescriptionCode
Methods description
overlapcode    nextTop
See documentation in Bio::Search::Hit::HitI::overlap()
ncodeprevnextTop
 Usage     : $hit_object->n();
Purpose : Gets the N number for the current 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.
Comments : 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()
hspcodeprevnextTop
 Usage     : $hit_object->hsp( [string] );
Purpose : Get a single HSPI object for the present HitI 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()
rankcodeprevnextTop
 Title   : rank
Usage : $obj->rank($newval)
Function: Get/Set the rank of this Hit in the Query search list
i.e. this is the Nth hit for a specific query
Returns : value of rank
Args : newvalue (optional)
locuscodeprevnextTop
 Title   : locus
Usage : $locus = $hit->locus();
Function: Retrieve the locus (if available) for the hit
Returns : a scalar string (empty string if not set)
Args : none
each_accession_numbercodeprevnextTop
 Title   : each_accession_number
Usage : @each_accession_number = $hit->each_accession_number();
Function: Get each accession number listed in the description of the hit.
If there are no alternatives, then only the primary accession will
be given
Returns : list of all accession numbers in the description
Args : none
query_lengthcodeprevnextTop
 Title   : query_length
Usage : $obj->query_length($newval)
Function: Get/Set the query_length
Returns : value of query_length (a scalar)
Args : on set, new value (a scalar or undef, optional)
ncbi_gicodeprevnextTop
 Title   : ncbi_gi
Usage : $acc = $hit->ncbi_gi();
Function: Retrieve the NCBI Unique ID (aka the GI #),
if available, for the hit
Returns : a scalar string (empty string if not set)
Args : none
length_alncodeprevnextTop
gapscodeprevnextTop
matchescodeprevnextTop
startcodeprevnextTop
endcodeprevnextTop
rangecodeprevnextTop
frac_identicalcodeprevnextTop
frac_conservedcodeprevnextTop
frac_aligned_querycodeprevnextTop
frac_aligned_hitcodeprevnextTop
num_unaligned_hitcodeprevnextTop
num_unaligned_querycodeprevnextTop
seq_indscodeprevnextTop
strandcodeprevnextTop
framecodeprevnextTop
logical_lengthcodeprevnextTop
Methods code
overlapdescriptionprevnextTop
sub overlap {
    my $self = shift;
    if(@_) { $self->{'_overlap'} = shift; }
    defined $self->{'_overlap'} ? $self->{'_overlap'} : 0;
}
ndescriptionprevnextTop
sub n {
    my $self = shift;

    $self->{'_n'} = shift if @_;

    if (defined $self->{'_n'}) {
        return $self->{'_n'}
    } else {
        return $self->num_hsps;
    }
}
hspdescriptionprevnextTop
sub hsp {
    my( $self, $option ) = @_;
    $option ||= 'best';

    if (not ref $self->{'_hsps'}) {
        $self->throw("Can't get HSPs: data not collected.");
    }

    my @hsps = $self->hsps;

    return $hsps[0]      if $option =~ /best|first|1/i;
    return $hsps[$#hsps] if $option =~ /worst|last/i;

    $self->throw("Can't get HSP for: $option\n" .
                 "Valid arguments: 'best', 'worst'");
}
rankdescriptionprevnextTop
sub rank {
    my $self = shift;
    return $self->{'_rank'} = shift if @_;
    return $self->{'_rank'} || 1;
}
locusdescriptionprevnextTop
sub locus {
    my ($self,$value) = @_;
    my $previous = $self->{'_locus'};
    if( defined $value || ! defined $previous ) {
      unless (defined $value) {
        if ($self->{'_name'} =~/(gb|emb|dbj|ref)\|(.*)\|(.*)/) {
                  $value = $previous = $3;
                } else {
          $value = $previous = '';
        }
      }
          $self->{'_locus'} = $value;
    }
        return $previous;
}
each_accession_numberdescriptionprevnextTop
sub each_accession_number {
    my ($self,$value) = @_;
    my $desc = $self->{'_description'};
    #put primary accnum on the list
my @accnums; push (@accnums,$self->{'_accession'}); if( defined $desc ) { while ($desc =~ /(\b\S+\|\S*\|\S*\s?)/g) { my $id = $1; my ($acc, $version); if ($id =~ /(gb|emb|dbj|sp|pdb|bbs|ref|tp[gde])\|(.*)\|(.*)/) { ($acc, $version) = split /\./, $2; } elsif ($id =~ /(pir|prf|pat|gnl)\|(.*)\|(.*)/) { ($acc, $version) = split /\./, $3; } elsif( $id =~ /(gim|gi|bbm|bbs|lcl)\|(\d*)/) { $acc = $id; } elsif( $id =~ /(oth)\|(.*)\|(.*)\|(.*)/ ) { # discontinued...
($acc,$version) = ($2); } else { #punt, not matching the db's at ftp://ftp.ncbi.nih.gov/blast/db/README
#Database Name Identifier Syntax
#============================ ========================
#GenBank gb|accession|locus
#EMBL Data Library emb|accession|locus
#DDBJ, DNA Database of Japan dbj|accession|locus
#NBRF PIR pir||entry
#Protein Research Foundation prf||name
#SWISS-PROT sp|accession|entry name
#Brookhaven Protein Data Bank pdb|entry|chain
#Patents pat|country|number
#GenInfo Backbone Id bbs|number
#General database identifier gnl|database|identifier
#NCBI Reference Sequence ref|accession|locus
#Local Sequence identifier lcl|identifier
$acc=$id; } push(@accnums, $acc); } } return @accnums;
}
query_lengthdescriptionprevnextTop
sub query_length {
    my $self = shift;

    return $self->{'_query_length'} = shift if @_;
    return $self->{'_query_length'};
}
ncbi_gidescriptionprevnextTop
sub ncbi_gi {
    my ($self,$value) = @_;
    my $previous = $self->{'_ncbi_gi'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{'_ncbi_gi'} = $value;
    }
        return $previous;
}
length_alndescriptionprevnextTop
sub length_aln {
    my $self = shift;
    $self->warn('$hit->length_aln not implemented for Model-based searches');
    return;
}
gapsdescriptionprevnextTop
sub gaps {
    my $self = shift;
    $self->warn('$hit->gaps not implemented for Model-based searches');
    return;
}
matchesdescriptionprevnextTop
sub matches {
    my $self = shift;
    $self->warn('$hit->matches not implemented for Model-based searches');
    return;
}
startdescriptionprevnextTop
sub start {
    my $self = shift;
    $self->warn('$hit->start not implemented for Model-based searches');
    return;
}
enddescriptionprevnextTop
sub end {
    my $self = shift;
    $self->warn('$hit->end not implemented for Model-based searches');
    return;
}
rangedescriptionprevnextTop
sub range {
    my $self = shift;
    $self->warn('$hit->range not implemented for Model-based searches');
    return;
}
frac_identicaldescriptionprevnextTop
sub frac_identical {
    my $self = shift;
    $self->warn('$hit->frac_identical not implemented for Model-based searches');
    return;
}
frac_conserveddescriptionprevnextTop
sub frac_conserved {
    my $self = shift;
    $self->warn('$hit->frac_conserved not implemented for Model-based searches');
    return;
}
frac_aligned_querydescriptionprevnextTop
sub frac_aligned_query {
    my $self = shift;
    $self->warn('$hit->frac_aligned_query not implemented for Model-based searches');
    return;
}
frac_aligned_hitdescriptionprevnextTop
sub frac_aligned_hit {
    my $self = shift;
    $self->warn('$hit->frac_aligned_hit not implemented for Model-based searches');
    return;
}
num_unaligned_hitdescriptionprevnextTop
sub num_unaligned_hit {
    my $self = shift;
    $self->warn('$hit->num_unaligned_hit/num_unaligned_sbjct not implemented for Model-based searches');
    return;
}
num_unaligned_querydescriptionprevnextTop
sub num_unaligned_query {
    my $self = shift;
    $self->warn('$hit->num_unaligned_query not implemented for Model-based searches');
    return;
}
seq_indsdescriptionprevnextTop
sub seq_inds {
    my $self = shift;
    $self->warn('$hit->seq_inds not implemented for Model-based searches');
    return;
}
stranddescriptionprevnextTop
sub strand {
    my $self = shift;
    $self->warn('$hit->strand not implemented for Model-based searches');
    return;
}
framedescriptionprevnextTop
sub frame {
    my $self = shift;
    $self->warn('$hit->frame not implemented for Model-based searches');
    return;
}
logical_lengthdescriptionprevnextTop
sub logical_length {
    my $self = shift;
    $self->warn('$hit->logical_length not implemented for Model-based searches');
    return;
}

1;
}
General documentation
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
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
SupportTop
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
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chris FieldsTop
Email cjfields at bioperl dot org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
HitI methods implemented in parent class Bio::Search::Hit::ModelHitTop
newTop
 Title   : new
Usage : my $obj = Bio::Search::Hit::ModelHit->new();
Function: Builds a new Bio::Search::Hit::ModelHit object
Returns : Bio::Search::Hit::ModelHit
Args : -name => Name of Hit (required)
-description => Description (optional)
-accession => Accession number (optional)
-ncbi_gi => NCBI GI UID (optional)
-length => Length of the Hit (optional)
-score => Raw Score for the Hit (optional)
-bits => Bit Score for the Hit (optional)
-significance => Significance value for the Hit (optional)
-algorithm => Algorithm used (BLASTP, FASTX, etc...)
-hsps => Array ref of HSPs for this Hit.
-found_again => boolean, true if hit appears in a
"previously found" section of a PSI-Blast report.
-hsp_factory => Bio::Factory::ObjectFactoryI able to create HSPI
objects.
add_hspTop
 Title   : add_hsp
Usage : $hit->add_hsp($hsp)
Function: Add a HSP to the collection of HSPs for a Hit
Returns : number of HSPs in the Hit
Args : Bio::Search::HSP::HSPI object, OR hash ref containing data suitable
for creating a HSPI object (&hsp_factory must be set to get it back)
hsp_factoryTop
 Title   : hsp_factory
Usage : $hit->hsp_factory($hsp_factory)
Function: Get/set the factory used to build HSPI objects if necessary.
Returns : Bio::Factory::ObjectFactoryI
Args : Bio::Factory::ObjectFactoryI
Bio::Search::Hit::HitI methodsTop
Implementation of Bio::Search::Hit::HitI methods
nameTop
 Title   : name
Usage : $hit_name = $hit->name();
Function: returns the name of the Hit sequence
Returns : a scalar string
Args : [optional] scalar string to set the name
accessionTop
 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
descriptionTop
 Title   : description
Usage : $desc = $hit->description();
Function: Retrieve the description for the hit
Returns : a scalar string
Args : [optional] scalar string to set the descrition
lengthTop
 Title   : length
Usage : my $len = $hit->length
Function: Returns the length of the hit
Returns : integer
Args : [optional] integer to set the length
algorithmTop
 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 : [optional] scalar string to set the algorithm
raw_scoreTop
 Title   : raw_score
Usage : $score = $hit->raw_score();
Function: Gets the "raw score" generated by the algorithm. What
this score is exactly will vary from algorithm to algorithm,
returning undef if unavailable.
Returns : a scalar value
Args : [optional] scalar value to set the raw score
scoreTop
Equivalent to raw_score()
significanceTop
 Title   : significance
Usage : $significance = $hit->significance();
Function: Used to obtain the E or P value of a hit, i.e. the probability that
this particular hit was obtained purely by random chance. If
information is not available (nor calculatable from other
information sources), return undef.
Returns : a scalar value or undef if unavailable
Args : [optional] scalar value to set the significance
bitsTop
 Usage     : $hit_object->bits();
Purpose : Gets the bit score of the best HSP for the current hit.
Example : $bits = $hit_object->bits();
Returns : Integer or undef if bit score is not set
Argument : n/a
Comments : For BLAST1, the non-bit score is listed in the summary line.
See Also : score()
next_hspTop
 Title    : next_hsp
Usage : while( $hsp = $obj->next_hsp()) { ... }
Function : Returns the next available High Scoring Pair
Example :
Returns : Bio::Search::HSP::HSPI object or null if finished
Args : none
hspsTop
 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()
num_hspsTop
 Usage     : $hit_object->num_hsps();
Purpose : Get the number of HSPs for the present hit.
Example : $nhsps = $hit_object->num_hsps();
Returns : Integer or '-' if HSPs have not been callected
Argument : n/a
See Also : hsps()
rewindTop
 Title   : rewind
Usage : $hit->rewind;
Function: Allow one to reset the HSP iterator to the beginning
Since this is an in-memory implementation
Returns : none
Args : none
ambiguous_alnTop
 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
Comment : Note: "sbjct" is synonymous with "hit"
pTop
 Usage     : $hit_object->p( [format] );
Purpose : Get the P-value for the best HSP
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::SearchUtils::get_exponent()
tiled_hspsTop
See documentation in Bio::Search::SearchUtils::tile_hsps()
ModelHit methods overridden in ModelHitTop
The following methods have been overridden due to their current reliance on
sequence-based queries. They may be implemented in future versions of this class.