/ 
Bio-DOOP-DOOP-1.00
/ Bio::DOOP::Util::Run::Fuzznuc

NAME

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

VERSION

Version 0.4

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,"/data/DOOP/dummy.txt");

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

$error = $fuzznuc->run('TTGGGC' , 1 , 0);

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

@res = @{$fuzznuc->get_results}; for $result (@res){ print $$result[0]->get_id,"| ",$$result[1]," ",$$result[2]," ",$$result[3]," ",$$result[4],"\n"; }

DESCRIPTION

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

patterns in the promoter sequences.

AUTHORS

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

SUBRUTINES

new

$fuzznuc = Bio::DOOP::Util::Run::Fuzznuc->new($db,500,'M',@list,'/tmp/tmpfile');
Create new Fuzznuc object.
Arguments: Bio::DOOP::DBSQL object, promoter type (500, 1000, 3000), subset type (depends on reference species),
listref of clusters, temp file name (default: /tmp/fuzznuc_run.txt).

new_by_file

Create new fuzznuc object from query file.
Arguments: Bio::DOOP::DBSQL object, promoter type (500, 1000, 3000), subset type (depends on reference species),
file that contain cluster ids, temp file name (default: /tmp/fuzznuc_run.txt).

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

get_emboss_version

Get the installed emboss version number
$fuzznuc->get_emboss_version

run

Run mofext on temporary file, containing motifs.
Arguments: query pattern, mismatch, complement (0 or 1).
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

Returns an arrayref of arrays of sequence objects.

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 fuzznuc objects. Maybe it is going to out from this module
in the future.