Bio::Tools::BPlite::HSP.3pm

Langue: en

Autres versions - même langue

Version: 2008-06-24 (ubuntu - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

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->seq_id;
             $hsp->hit->overlaps($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/wiki/Mailing_lists  - 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 the web:

   http://bugzilla.open-bio.org/
 
 

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)
 
 

EXP

  Title   : EXP
  Usage   : my $exp = $hsp->EXP;
  Function: returns the EXP value for the HSP
  Returns : string value
  Args    : none
  Note    : Patch provided by Sami Ashour for BTK parsing
 
 

P

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