Ewan Birney

NAME

Bio::Tools::BPlite::Sbjct - A Blast Subject (database search Hit)

SYNOPSIS

 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
     }

DESCRIPTION

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.

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/MailList.shtml  - About the mailing lists

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://bioperl.org/bioperl-bugs/

AUTHOR - Peter Schattner

Email: schattner@alum.mit.edu

CONTRIBUTORS

Jason Stajich, jason@cgt.mc.duke.edu

APPENDIX

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