Bio::Tools::BPbl2seq.3pm

Langue: en

Version: 2008-01-11 (mandriva - 01/05/08)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::BPbl2seq - Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm.

SYNOPSIS

   use Bio::Tools::BPbl2seq;
   my $report = Bio::Tools::BPbl2seq->new(-file => 't/bl2seq.out');
   $report->sbjctName;
   $report->sbjctLength;
   while(my $hsp = $report->next_feature) {
          $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->sbjct->start;
          $hsp->sbjct->end;
          $hsp->sbjct->seq_id;
          $hsp->sbjct->overlaps($exon);
  }
 
 

DESCRIPTION

NOTE: This module's functionality has been implemented in Bio::SearchIO::blast and therefore is not actively maintained.

BPbl2seq is a package for parsing BLAST bl2seq reports. BLAST bl2seq is a program for comparing and aligning two sequences using BLAST. Although the report format is similar to that of a conventional BLAST, there are a few differences so that BPlite is unable to read bl2seq reports directly.

From the user's perspective, one difference between bl2seq and other blast reports is that the bl2seq report does not print out the name of the first of the two aligned sequences. (The second sequence name is given in the report as the name of the ``hit''). Consequently, BPbl2seq has no way of identifying the name of the initial sequence unless it is passed to constructor as a second argument as in:

         my $report = Bio::Tools::BPbl2seq->new(\*FH, "ALEU_HORVU");
 
 

If the name of the first sequence (the ``query'') is not passed to BPbl2seq.pm in this manner, the name of the first sequence will be left as ``unknown''. (Note that to preserve a common interface with the other BLAST programs the two sequences being compared are referred to in bl2seq as ``query'' and ``subject'' although this is perhaps a bit misleading when simply comparing 2 sequences as opposed to querying a database.)

In addition, since there will only be (at most) one ``subject'' (hit) in a bl2seq report, one should use the method $report->next_feature, rather than $report->nextSbjct->nextHSP to obtain the next high scoring pair.

One should note that the previous (0.7) version of BPbl2seq used slightly different syntax. That version had a bug and consequently the old syntax has been eliminated. Attempts to use the old syntax will return error messages explaining the (minor) recoding required to use the current syntax.

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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web:

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

AUTHOR - Peter Schattner

Email: schattner@alum.mit.edu

ACKNOWLEDGEMENTS

Based on work of: Ian Korf (ikorf@sapiens.wustl.edu, http://sapiens.wustl.edu/~ikorf), Lorenz Pollak (lorenz@ist.org, bioperl port)

CONTRIBUTORS

Jason Stajich, jason-at-bioperl.org

new

  Title   : new
  Function: Create a new Bio::Tools::BPbl2seq object
  Returns : Bio::Tools::BPbl2seq
  Args    : -file     input file (alternative to -fh)
            -fh       input stream (alternative to -file)
            -queryname    name of query sequence
            -report_type What type of BLAST was run (blastn,blastp,tblastn...)
 
 

getSbjct

  Title    :
  Usage    : $sbjct = $obj->getSbjct();
  Function : Method of obtaining single "subject" of a bl2seq report
  Example  : my $sbjct = $obj->getSbjct ) {}
  Returns  : Sbjct object or undef if finished
  Args     :
 
 

next_feature

  Title   : next_feature
  Usage   : while( my $feat = $res->next_feature ) { # do something }
  Function: calls next_feature function from BPlite.
  Example :
  Returns : A Bio::SeqFeatureI compliant object, in this case a
            Bio::Tools::BPlite::HSP object, and FALSE if there are no more
            HSPs.
  Args    : None
 
 

queryName

  Title    :
  Usage    : $name = $report->queryName();
  Function : get /set the name of the query
  Example  :
  Returns  : name of the query
  Args     :
 
 

sbjctName

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

sbjctLength

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

P

  Title    : P
  Usage    :
  Function : Syntax no longer supported, error message only
 
 

percent

  Title    : percent
  Usage    : $hsp->percent();
  Function : Syntax no longer supported, error message only
 
 

match

  Title    : match
  Usage    : $hsp->match();
  Function : Syntax no longer supported, error message only
 
 

positive

  Title    : positive
  Usage    : $hsp->positive();
  Function : Syntax no longer supported, error message only
 
 

querySeq

  Title    : querySeq
  Usage    : $hsp->querySeq();
  Function : Syntax no longer supported, error message only
 
 

sbjctSeq

  Title    : sbjctSeq
  Usage    : $hsp->sbjctSeq();
  Function : Syntax no longer supported, error message only
 
 

homologySeq

  Title    : homologySeq
  Usage    : $hsp->homologySeq();
  Function : Syntax no longer supported, error message only
 
 

qs

  Title    : qs
  Usage    : $hsp->qs();
  Function : Syntax no longer supported, error message only
 
 

ss

  Title    : ss
  Usage    : $hsp->ss();
  Function : Syntax no longer supported, error message only
 
 

hs

  Title    : hs
  Usage    : $hsp->hs();
  Function : Syntax no longer supported, error message only