NAME

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

VERSION

  Version 0.16

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");

$mofext = Bio::DOOP::Util::Run::Mofext->new($db,'500','M',\@list);

$mofext->set_tmp_file_name("/data/DOOP/dummy.txt");

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

$error = $mofext->write_to_tmp;

if($error != 0){ die "Write error!\n"; }

$error = $mofext->run('TTGGGC' , 6 , 0.6 , '/data/default_matrix' );

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

@res = @{$mofext->get_results}; # Returns the motif objects, score and extended score. for $result (@res){ print $$result[0]->get_id," ",$$result[1],"$$result[2]","\n"; }

DESCRIPTION

  Mofext is a fuzzy sequence pattern search tool developed by Tibor Nagy. This module 
  is a wrapper object for mofext. It allows the user to search for similar motifs in the 
  DOOP database.

AUTHORS

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

METHODS

new

  Create a new Mofext object.

  Arguments :

  DBSQL object
  promoter type (500,1000,3000)
  subset type (B,E,M,V in plants)
  arrayref of cluster ids

new_by_file

  Create a new Mofext object from query file, containing cluster ids.

  Arguments :

  DBSQL object
  promoter type (500, 1000, 3000)
  subset type (B,E,M,V in plants)
  name of the file with cluster ids

new_by_tmp

  Create a new Mofext object from an existing temporary file. It is useful when you have a temporary file,
  and you want to use it over and over, or your temporary file is large (the new constructor is very slow when you use
  large cluster lists). If you use this constructor, you don't need to use the set_tmp_file_name and write_to_tmp 
  methods.

  Arguments :

  Bio::DOOP::DBSQL object
  temporary file name

  Example:

  use Bio::DOOP::DOOP
  $db      = Bio::DOOP::DBSQL->connect("user","pass","doop-chordate-1_4","localhost");

  $mofext = Bio::DOOP::Util::Run::Mofext->new_by_tmp($db,"/data/DOOP/temp.txt");
  $ret = $mofext->run('GGATCCTGGAT',10,0.95,'default_matrix.txt');
  @res = @{$mofext->get_results};

  for $res (@res){
    print $$res[0]->get_id," ",$$res[1],"\n";
  }

get_tmp_file_name

  Get the temporary file name.

  Return type :

  string

set_tmp_file_name

  Set the temporary file name.

  Arguments :

  temporary file name

write_to_tmp

  Write out the collected motifs to the temporary file.

  Return type :

  0 if success, -1 in case of error.

run

  Run mofext on temporary file, containing motifs.

  Arguments :

  query sequence
  wordsize
  cutoff
  matrix file path/name

  Return type :

  0 if success, -1 in case of no result or error.

run_background

  Run mofext, but do not wait for it to finish.

  Arguments :

  query sequence
  wordsize
  cutoff
  matrix file path/name
  output file path/name

  Return type :

  process id

get_results

  Returns an arrayref of arrays containing the following :

  motif object
  score
  extended score
  full hit sequence
  alignment start position in the query sequence
  alignment start position in the hit sequence

  for each hit

get_results_from_file

  Returns an arrayref of arrays containing the following :

  motif object
  score
  extended score
  full hit sequence
  alignment start position in the query sequence
  alignment start position in the hit sequence

  for each hit or -1 in case of errors

  This is a very uniq method because it does not depend on the object. So you can fetch
  results of different mofext objects.

cpanm Bio::DOOP::DOOP

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