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.