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.

cpanm Bio::DOOP::DOOP

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