NAME
Bio::DOOP::Util::Run::Mofext - Mofext runner module
VERSION
Version 0.08
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");
$mofext = Bio::DOOP::Util::Run::Mofext->new($db,'500',\@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}; # Return the cluster object and the motif primary id for $result (@res){ print $$result[0]->get_id," ",$$result[1],"\n"; }
DESCRIPTION
Mofext is a motif search utility developed by Tibor Nagy. This module is a wrapper
object for this tool. Is is allowed to the user to search similar motifs in the
DOOP database.
AUTHOR
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
SUBRUTINES
new
Create a new Mofext running object.
Arguments: DBSQL object, promoter type (500,1000,3000), listref of cluster id
new_by_file
Create a new Mofext running object from a file.
Arguments: DBSQL object, promoter type (500, 1000, 3000), filename of the cluster ids
get_tmp_file_name
Get the temporary file name.
Return type: string
set_tmp_file_name
Set the temporary file name.
Return type: none
write_to_tmp
Write out the collected motifs to the temporary file.
This step is important for mofext.
Return type: 0 -> success -1 -> error
run
Run program mofext in temporary file
Arguments: query seq, wordsize, cutoff, matrix file name
Return type: 0 -> success, -1 -> no results or error
get_results
Returns the arrayref of array of cluster objects and motif primary ids