NAME
Bio::DOOP::Util::Run::Mofext - Mofext runner module.
VERSION
Version 0.14
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','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}; # Return the motif objects and the score, extended score. for $result (@res){ print $$result[0]->get_id," ",$$result[1],"$$result[2]","\n"; }
DESCRIPTION
Mofext is a fuzzy sequence pattern search tool developed by Tibor Nagy. This module
is a wrapper object for mofext. It allows the user to search for similar motifs in the
DOOP database.
AUTHOR
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
SUBRUTINES
new
Create a new Mofext object.
Arguments: DBSQL object, promoter type (500,1000,3000), subset type (B,M,E,V in plants) arrayref of cluster ids.
new_by_file
Create a new Mofext object from a file.
Arguments: DBSQL object, promoter type (500, 1000, 3000), subset type (B,M,E,V in plants), name of the file with cluster ids.
new_by_tmp
Create a new Mofext object from a existed tmp file. It is good when you have a tmp file, and you want
to use it over and over again or your tmp file is large (the new constructor is very slow when you use
big cluster list). If you use this constructor, you no need to use set_tmp_file_name, write_to_tmp.
Arguments: Bio::DOOP::DBSQL object, temporary file name.
Return type: none
Example:
use Bio::DOOP::DOOP
$db = Bio::DOOP::DBSQL->connect("username","pswd","doop-chordate-1_4","localhost");
$mofext = Bio::DOOP::Util::Run::Mofext->new_by_tmp($db,"/adatok/prg/perl/DOOP/ize.txt");
$ret = $mofext->run('GGATCCTGGAT',10,0.95,'default_matrix.txt');
@res = @{$mofext->get_results};
for $res (@res){
print $$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
Return type: none
write_to_tmp
Write out the collected motifs to the temporary file.
Return type: 0 -> success, -1 -> error
run
Run mofext on temporary file, containing motifs.
Arguments: query sequence, wordsize, cutoff, matrix file path.
Return type: 0 -> success, -1 -> no result or error
run_background
Run mofext, but don not wait for the end
Arguents: query sequence, wordsize, cutoff, matrix file path, output file name
Return type: the process id
get_results
Returns the arrayref of array of cluster objects and motif primary ids.
get_results_from_file
Returns the arrayref of the array of cluster objects and motif primary ids or -1 in case
of error.
This is a very uniq method because it is not depend to the object. So you can fetch more
different results of different mofext objects. Maybe it is going to out from this module
in the future.