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.

cpanm Bio::DOOP::DOOP

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