Ewan Birney

NAME

Bio::Tools::BPlite::HSP - Blast report High Scoring Pair (HSP)

SYNOPSIS

 use Bio::Tools::BPlite;
 my $report = new Bio::Tools::BPlite(-fh=>\*STDIN);
 {
    while(my $sbjct = $report->nextSbjct) {
        while (my $hsp = $sbjct->nextHSP) {
            $hsp->score;
            $hsp->bits;
            $hsp->percent;
            $hsp->P;
            $hsp->match;
            $hsp->positive;
            $hsp->length;
            $hsp->querySeq;
            $hsp->sbjctSeq;
            $hsp->homologySeq;
            $hsp->query->start;
            $hsp->query->end;
            $hsp->hit->start;
            $hsp->hit->end;
            $hsp->hit->seqname;
            $hsp->hit->overlaps($exon);
        }
    }

    # the following line takes you to the next report in the stream/file
    # it will return 0 if that report is empty,
    # but that is valid for an empty blast report.
    # Returns -1 for EOF.

    last if ($report->_parseHeader == -1));

 redo
 }

DESCRIPTION

This object handles the High Scoring Pair data for a Blast report. This is where the percent identity, query and hit sequence length, P value, etc are stored and where most of the necessary information is located when building logic around parsing a Blast report.

See Bio::Tools::BPlite for more detailed information on the entire BPlite Blast parsing system.

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@bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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)

P

 Title    : P
 Usage    : $hsp->P();
 Function : returns the P (significance) value for a HSP 
 Example  : 
 Returns  : (double) significance value
 Args     :

percent

 Title    : percent
 Usage    : $hsp->percent();
 Function : returns the percent matching 
 Returns  : (double) percent matching
 Args     : none

match

 Title    : match
 Usage    : $hsp->match();
 Function : returns the match
 Example  : 
 Returns  : (double) frac_identical 
 Args     :

hsplength

 Title    : hsplength
 Usage    : $hsp->hsplength();
 Function : returns the HSP length (including gaps)
 Returns  : (integer) HSP length
 Args     : none

positive

 Title    : positive
 Usage    : $hsp->positive();
 Function : returns the number of positive matches (symbols in the alignment
            with a positive score)
 Returns  : (int) number of positive matches in the alignment
 Args     : none

gaps

 Title    : gaps
 Usage    : $hsp->gaps();
 Function : returns the number of gaps or 0 if none
 Returns  : (int) number of gaps or 0 if none
 Args     : none

querySeq

 Title    : querySeq
 Usage    : $hsp->querySeq();
 Function : returns the query sequence
 Returns  : (string) the Query Sequence 
 Args     : none

sbjctSeq

 Title    : sbjctSeq
 Usage    : $hsp->sbjctSeq();
 Function : returns the Sbjct sequence 
 Returns  : (string) the Sbjct Sequence 
 Args     : none

homologySeq

 Title    : homologySeq
 Usage    : $hsp->homologySeq();
 Function : returns the homologous sequence 
 Returns  : (string) homologous sequence 
 Args     : none

qs

 Title    : qs
 Usage    : $hsp->qs();
 Function : returns the Query Sequence (same as querySeq)
 Returns  : (string) query Sequence 
 Args     : none

ss

 Title    : ss
 Usage    : $hsp->ss();
 Function : returns the subject sequence ( same as sbjctSeq) 
 Returns  : (string) Sbjct Sequence
 Args     : none

hs

 Title    : hs
 Usage    : $hsp->hs();
 Function : returns the Homologous Sequence (same as homologySeq ) 
 Returns  : (string) Homologous Sequence
 Args     : none