/ 
Bio-DOOP-DOOP-0.26
/ Bio::DOOP::Util::Run::Fuzznuc

NAME

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

VERSION

Version 0.2

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");

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

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

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

$error = $fuzznuc->write_to_tmp;

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

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

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

@res = @{$fuzznuc->get_results};

DESCRIPTION

This module is a wrapper for the Emboss program fuzznuc. You can search

patterns in the promoter sequences.

AUTHOR

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

SUBRUTINES

new

new_by_file

Create new fuzznuc object from query file.

new_by_tmp

Create new Fuzznuc object from existing tmp file. It is good for
speed up the search with previously created tmp file.
Arguments: DBSQL object, tmp filename.

get_tmp_file_name

Get the temporary file name.
Return type: string

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 fuzznuc, but don not wait for the end
Arguents: query pattern, mismatch, complement, output file name
Return type: the process id

get_results_from_file

Returns ... 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.