Copyright Notice

 Copyright I.N.R.A. - C.N.R.S.
 emmanuel.courcelle@toulouse.inra.fr
 jerome.gouzy@toulouse.inra.fr
 This software is a computer program whose purpose is to help you run 
 your scripts on parallel computers.
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NAME

PARALOOP::PLUGIN::Blast - Executing blast (any version)


Derives from...

PARALOOP::PLUGIN::BpInput


DESCRIPTION

This plugin reads the next record from the fasta input file, uses this file as a query for a blastall -p request agains the bank, passed through the --db switch The tabular output is chosen


CONFIGURATION FILE PARAMETERS

 PARALOOP_Blast_origin 
     ncbi or wu: both are supported, but default is ncbi
 PARALOOP_Blast_path
     path to the binary program (default blastall if ncbi, blastp if wu)
 PARALOOP_Blast_params
     Parameters for blast (default -p blastp if ncbi, nothing if wu)
 PARALOOP_Blast_chunk
     Group requests in chunks for a better efficiency (default 1, ie not grouped)


PUBLIC METHODS

 WhatParaloopPlugin
      my $msg=$obj->WhatParaloopPlugin()
 Parameters
      my $msg=$obj->Parameters()
 New
      my $obj = PARALOOP::Dummy->New(-params => $params, -log => $o_log);
 Exec
      my ($incr_size,$error,$killed) = $obj->Exec();
 SetOutputFile
      $obj->SetOutputFile('filename');


METHODS AND SUBROUTINES - DETAILED DESCRIPTION

Function WhatParaloopPlugin

 Usage:    my $msg = PARALOOP::Dummy::WhatParaloopPlugin()
        or my $msg = $obj->WhatParaloopPlugin()
 Function: Return some information (2 lines max) on the plugin
           An object is NOT considered as a plugin if this function is not implemented
 Arg:      none ($self is ignored)
 Return:   A message describing the plugin (1 or 2 lines)

Function Parameters

 Usage:    my $msg = PARALOOP::Dummy::Parameters()
        or my $msg = $obj->Parameters()
 Function: Return the list of allowed parameters for this plugin
           If your plugin defines some parameters, it is good pratice adding this function,
           to display those parameters when the --parameters switch of paraloop.pl is used.
           However, this is not mandatory
 Arg:      none ($self is ignored)
 Return:   A message describing the plugin (1 or 2 lines)

procedure __Init

 Usage:  CALLED BY _Initializable::New
         my obj = PARALOOP::Dummy->New(-params => $params, -log => $o_log);
 Access: private (use New instead)
 procedure: Init the object
 Return:   nothing
 Args:     -params = an object of class ParamParser (already initialized)
           -log    = an object of class Logger (already initialized)
 globals:  none

Procedure SetOutputFile

 Usage:     &$opt->SetOutputFile('filename');
 Procedure: change the name of the output file
 Arg :      the output file name

Function Exec

 Usage:    my ($incr_size, $error,$killed) = &$opt->Exec($timeout);
 Function: Execute a blast
 Arg:      $timeout   = The number of seconds after which a timeout is sent
 Return:   $incr_size = The number of bytes added to the output file
           $error     = An error code. 
                                If != 0, paraloop WILL BE TERMINATED - Generally marks the end of file
           $killed    = A kill code
                                0: everything OK 
                       -1: killed by timeout
                       -2: killed by TERM signal (kill, qdel, ...)

Function __SingleSeq

 Usage:    my ($incr_size, $error,$killed) = &self->__SingleSeq($timeout);
 Function: Called by Exec when blasts are made sequence by sequence
 Arg, Return: see Exec

Function __SingleSeq

 Usage:    my ($incr_size, $error,$killed) = &self->__SeveralSeq($timeout);
 Function: Called by Exec when blasts are made in chunks of sequences
 Arg, Return: see Exec