Bio::Tools::BPlite::Sbjct - A Blast Subject (database search Hit) use Bio::Tools::BPlite; my $report = new Bio::Tools::BPlite(-fh=>\*STDIN); while(my $sbjct = $report->nextSbjct) { $sbjct->name; # access to the hit name "$sbjct"; # overloaded to return name $sbjct->nextHSP; # gets the next HSP from the sbjct while (my $hsp = $sbjct->nextHSP) { # canonical form is again a while loop } } See Bio::Tools::BPlite for a more detailed information about the BPlite BLAST parsing objects. The original BPlite.pm module has been written by Ian Korf! See http://sapiens.wustl.edu/~ikorf The Sbjct object encapsulates a Hit in a Blast database search. The Subjects are the "Hits" for a particular query. A Subject may be made up of multiple High Scoring Pairs (HSP) which are accessed through the nextHSP method. If you are searching for the P-value or percent identity that is specific to each HSP and you will need to use the nextHSP method to get access to that data.

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email: schattner@alum.mit.edu Jason Stajich, jason@cgt.mc.duke.edu The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

name
Title : name Usage : $name = $obj->name(); Function : returns the name of the Sbjct Example : Returns : name of the Sbjct Args :

report_type
Title : report_type Usage : $type = $sbjct->report_type() Function : Returns the type of report from which this hit was obtained. This usually pertains only to BLAST and friends reports, for which the report type 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). Example : Returns : A string (BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX, UNKNOWN) Args : a string on set (you should know what you are doing)

nextFeaturePair
Title : nextFeaturePair Usage : $name = $obj->nextFeaturePair(); Function : same as the nextHSP function Example : Returns : next FeaturePair Args :

nextHSP
Title : nextHSP Usage : $hsp = $obj->nextHSP(); Function : returns the next available High Scoring Pair Example : Returns : Bio::Tools::HSP or null if finished Args :

_readline
Title : _readline Usage : $obj->_readline Function: Reads a line of input. Note that this method implicitely uses the value of $/ that is in effect when called. Note also that the current implementation does not handle pushed back input correctly unless the pushed back input ends with the value of $/. Example : Returns :

_pushback
Title : _pushback Usage : $obj->_pushback($newvalue) Function: puts a line previously read with _readline back into a buffer Example : Returns : Args : newvalue