/ 
bioperl-1.0.2
/ Bio::Tools::BPlite::HSP

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