/ 
Bio-DOOP-DOOP-0.08
/ Bio::DOOP::Util::Run::Mofext

NAME

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

VERSION

Version 0.08

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 object and the motif primary id for $result (@res){ print $$result[0]->get_id," ",$$result[1],"\n"; }

DESCRIPTION

Mofext is a motif search utility developed by Tibor Nagy. This module is a wrapper
object for this tool. Is is allowed to the user to search similar motifs in the 
DOOP database.

AUTHOR

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

SUBRUTINES

new

Create a new Mofext running object.
Arguments: DBSQL object, promoter type (500,1000,3000), listref of cluster id

new_by_file

Create a new Mofext running object from a file.
Arguments: DBSQL object, promoter type (500, 1000, 3000), filename of the 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.
This step is important for mofext.
Return type: 0 -> success -1 -> error

run

Run program mofext in temporary file
Arguments: query seq, wordsize, cutoff, matrix file name
Return type: 0 -> success, -1 -> no results or error

get_results

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