NAME

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

VERSION

  Version 0.5

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");

$fuzznuc = Bio::DOOP::Util::Run::Fuzznuc->new($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 with it.

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

  Creates 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

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

get_tmp_file_name

  Get the temporary file name.
  Return type: string

get_emboss_version

  $fuzznuc->get_emboss_version

  Get the installed emboss version number

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 do not wait for the search to finish.
  Arguents: query pattern, mismatch, complement, output file name
  Return type: the process id

get_results

  Returns an arrayref of arrays of cluster objects.

get_results_from_file

  Returns ... or -1 in case
  of error.
  This is a very uniq method because it does not depend on the object. So you can fetch
  different results of different mofext objects.

cpanm Bio::DOOP::DOOP

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