/ 
Bio-DOOP-DOOP-1.01
/ Bio::DOOP::Util::Run::Mofext

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.