/ 
Bio-DOOP-DOOP-1.02
/ 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");

$fuzznuc = Bio::DOOP::Util::Run::Fuzznuc->new($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 (http://emboss.sourceforge.net) program fuzznuc. You can search
patterns in the promoter sequences.

AUTHORS

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

METHODS

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)
arrayref of clusters
temporary file name (default: /tmp/fuzznuc_run.txt)

new_by_file

Create new fuzznuc object from query file, containing cluster ids.

Arguments :

Bio::DOOP::DBSQL object
promoter type (500, 1000, 3000)
subset type (depends on reference species)
file that contain cluster ids
temporary file name (default: /tmp/fuzznuc_run.txt)

new_by_tmp

Create new Fuzznuc object from existing temporary file, containing query sequences in fasta format.

Arguments :

DBSQL object
temporary file name

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

Return type :

string

run

Run fuzznuc on temporary file, containing sequences.

Arguments :

query pattern
mismatch number
complement (0 or 1)

Return type :

0 if success, -1 if no results or error happened

run_background

Run fuzznuc, but do not wait for completion.

Arguments :

query pattern
mismatch number
complement (0 or 1)
output filename

Return type :

process id

get_raw_results

Returns an arrayref of arrays of the raw fuzznuc result without objects.
It is much faster because does not use the database.

get_results

Returns an arrayref of arrays of sequence objects.

get_results_from_file

Returns an arrayref of arrays of sequence objects or -1 if an error happened.

This is a very unique methods because it does not depend on the object. With it you can fetch
the results of different fuzznuc objects. Maybe it will go out from the module in the future.