NAME¶
Bio::Search::Hit::HMMERHit - A Hit module for HMMER hits
SYNOPSIS¶
use Bio::Search::Hit::HMMERHit;
my $hit = Bio::Search::Hit::HMMERHit->new();
# use it in the same way as Bio::Search::Hit::GenericHit
DESCRIPTION¶
This is a specialization of Bio::Search::Hit::GenericHit. There are a few news
methods next_domain and domains. Note that bits and iteration make no sense
for this object and will return 0.
FEEDBACK¶
Mailing Lists¶
User feedback is an integral part of the evolution of this and other Bioperl
modules. Send your comments and suggestions preferably to the Bioperl mailing
list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support¶
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive
experts will be able look at the problem and quickly address it. Please
include a thorough description of the problem with code and data examples if
at all possible.
Reporting Bugs¶
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs
and their resolution. Bug reports can be submitted via the web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich¶
Email jason@bioperl.org
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
new¶
Title : new
Usage : my $obj = Bio::Search::Hit::HMMERHit->new();
Function: Builds a new Bio::Search::Hit::HMMERHit object
Returns : Bio::Search::Hit::HMMERHit
Args :
Plus the Bio::Search::Hit::GenericHit inherited params
-name => Name of Hit (required)
-description => Description (optional)
-accession => Accession number (optional)
-length => Length of the Hit (optional)
-score => Raw 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.
next_domain¶
Title : next_domain
Usage : my $domain = $hit->next_domain();
Function: An alias for L<next_hsp()>, this will return the next HSP
Returns : L<Bio::Search::HSP::HSPI> object
Args : none
domains¶
Title : domains
Usage : my @domains = $hit->domains();
Function: An alias for L<hsps()>, this will return the full list of hsps
Returns : array of L<Bio::Search::HSP::HSPI> objects
Args : none
inherited Bio::Search::Hit::GenericHit methods¶
add_hsp¶
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
Bio::Search::Hit::HitI methods¶
name¶
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
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
description¶
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
length¶
Title : length
Usage : my $len = $hit->length
Function: Returns the length of the hit
Returns : integer
Args : [optional] integer to set the length
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 : [optional] scalar string to set the algorithm
raw_score¶
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
significance¶
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
bits¶
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
See Also :
score()
next_hsp¶
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
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()
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()
rewind¶
Title : rewind
Usage : $hit->rewind;
Function: Allow one to reset the HSP iteration to the beginning
Since this is an in-memory implementation
Returns : none
Args : none
iteration¶
Title : iteration
Usage : $obj->iteration($newval)
Function: PSI-BLAST iteration
Returns : value of iteration
Args : newvalue (optional)