NAME

  Bio::DOOP::Util::Run::Mofext - Mofext runner module.

VERSION

  Version 0.09

SYNOPSIS

#!/usr/bin/perl -w

use Bio::DOOP::DOOP $db = Bio::DOOP::DBSQL->connect("user","pass","doop-plant-1_5","localhost");

@list = ("81001020","81001110","81001200","81001225","81001230","81001290","81001470","81001580","81001610","81001620","81001680","81001680","81001690","81001725","81001780","81001930","81001950","81002100","81002130","81002140","81002160");

$mofext = Bio::DOOP::Util::Run::Mofext->new($db,'500',\@list);

$mofext->set_tmp_file_name("/data/DOOP/dummy.txt");

print $mofext->get_tmp_file_name,"\n";

$error = $mofext->write_to_tmp;

if($error != 0){ die "Write error!\n"; }

$error = $mofext->run('TTGGGC' , 6 , 0.6 , '/data/default_matrix' );

if ($error == -1){ die "No results or error!\n"; }

@res = @{$mofext->get_results}; # Return the cluster objects and the motif primary ids. for $result (@res){ print $$result[0]->get_id," ",$$result[1],"\n"; }

DESCRIPTION

  Mofext is a fuzzy sequence pattern search tool developed by Tibor Nagy. This module 
  is a wrapper object for mofext. It allows the user to search for similar motifs in the 
  DOOP database.

AUTHOR

  Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary

SUBRUTINES

new

  Create a new Mofext object.
  Arguments: DBSQL object, promoter type (500,1000,3000), arrayref of cluster ids.

new_by_file

  Create a new Mofext object from a file.
  Arguments: DBSQL object, promoter type (500, 1000, 3000), name of the file with cluster ids.

get_tmp_file_name

  Get the temporary file name.
  Return type: string

set_tmp_file_name

  Set the temporary file name.
  Return type: none

write_to_tmp

  Write out the collected motifs to the temporary file.
  Return type: 0 -> success, -1 -> error

run

  Run mofext on temporary file, containing motifs.
  Arguments: query sequence, wordsize, cutoff, matrix file path.
  Return type: 0 -> success, -1 -> no result or error

run_background

  Run mofext, but don not wait for the end
  Arguents: query sequence, wordsize, cutoff, matrix file path, output file name
  Return type: the process id

get_results

  Returns the arrayref of array of cluster objects and motif primary ids.

get_results_from_file

  Returns the arrayref of the array of cluster objects and motif primary ids or -1 in case
  of error.
  This is a very uniq methods because it is not depend to the object. So you can fetch more
  different results of different mofext objects. Maybe it is going to out from this module
  in the future.

cpanm Bio::DOOP::DOOP

perl -MCPAN -e shell
install Bio::DOOP::DOOP