Bio::Search::Hit::GenericHit - A generic implementation of the Bio::Search::Hit::HitI interface
{ use Bio::Search::Hit::GenericHit; my $hit = new Bio::Search::Hit::GenericHit(-algorithm => 'blastp'); }
This object handles the hit data from a Database Sequence Search such as FASTA or BLAST.
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/MailList.shtml - About the mailing lists
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 email or the web:
bioperl-bugs@bioperl.org http://bioperl.org/bioperl-bugs/
Email jason@bioperl.org Email sac@bioperl.org
Additional contributors names and emails here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = new Bio::Search::Hit::GenericHit(); Function: Builds a new Bio::Search::Hit::GenericHit object Returns : Bio::Search::Hit::GenericHit Args : -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.
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
Implementation of Bio::Search::Hit::HitI methods
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
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
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
Title : length Usage : my $len = $hit->length Function: Returns the length of the hit Returns : integer Args : [optional] integer to set the length
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
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
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
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
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
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()
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.