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.
 This software is governed by the CeCILL  license under French law and
 abiding by the rules of distribution of free software.  You can  use, 
 modify and/ or redistribute the software under the terms of the CeCILL
 license as circulated by CEA, CNRS and INRIA at the following URL
 http://www.cecill.info";
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 with a limited warranty  and the software's author,  the holder of the
 economic rights,  and the successive licensors  have only  limited
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 In this respect, the user's attention is drawn to the risks associated
 with loading,  using,  modifying and/or developing or reproducing the
 software by the user in light of its specific status of free software,
 that may mean  that it is complicated to manipulate,  and  that  also
 therefore means  that it is reserved for developers  and  experienced
 professionals having in-depth computer knowledge. Users are therefore
 encouraged to load and test the software's suitability as regards their
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NAME

PARALOOP::PLUGIN::Bioperl - Executing something with files read using bioperl


Derives from...

PARALOOP::PLUGIN::BpInput


DESCRIPTION

This plugin reads the next record from the input file, whose format must be recognized by bioperl, calls an external program or script, then writes the output of this program

The external script is passed as: script_name param1 param2 ... input output, ie the last two parameters are the input and the output file, the other parameters are declared by PARAMETER_Bioperl_params

Please note that when the script is ran, its current directory is a temporary directory, located in the same directory as the input file. You may securely create files here.


CONFIGURATION FILE PARAMETERS

 PARALOOP_Bioperl_path
     path to the external script, ran at each iteration. No default
 PARALOOP_Bioperl_params
     parameters passed to this script. Default 0
 PARALOOP_Bioperl_input_format
     Format for the input file (default to fasta)
     WARNING - This is the format to the file which is read by THE EXTERNAL script
               BUT the input file from paraloop may be of any format automatically recognized by bioperl


A very short example

The following is a very stupid script, which makes nothing which could be executed through this plugin:

 #!/bin/sh
 sleep $1;
 cat $2 > $3
 exit 0;

If the script is called stupid.sh and lives in the current paraloop directory, there should be two parameters defined:

 PARALOOP_Bioperl_path  = stupid.sh
 PARALOOP_Bioperl_params = 3

The script is called by paraloop as:

 stupid.sh 3 input output


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

procedure DESTROY

 Usage:     The destructor of the object
            undef($obj);
 Access:    public
 procedure: Destroyes the resources allocated by __Init
 Return:    nothing
 Args:      nothing
 globals:   none

Function Exec

 Usage:    my ($incr_size, $error,$killed) = &$opt->Exec($timeout);
 Function: Execute the external script
 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, ...)