NAME
Bio::DOOP::Util::Run::Fuzznuc - Fuzznuc runner module.
VERSION
Version 0.3
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");
$fuzznuc = Bio::DOOP::Util::Run::Fuzznuc->new($db,'500','M',\@list,"/data/DOOP/dummy.txt");
print $fuzznuc->get_tmp_file_name,"\n";
$error = $fuzznuc->run('TTGGGC' , 1 , 0);
if ($error == -1){ die "No results or error!\n"; }
@res = @{$fuzznuc->get_results}; for $result (@res){ print $$result[0]->get_id,"| ",$$result[1]," ",$$result[2]," ",$$result[3]," ",$$result[4],"\n"; }
DESCRIPTION
This module is a wrapper for the Emboss program fuzznuc. You can search
patterns in the promoter sequences.
AUTHORS
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
SUBRUTINES
new
$fuzznuc = Bio::DOOP::Util::Run::Fuzznuc->new($db,500,'M',@list,'/tmp/tmpfile');
Create new Fuzznuc object.
Arguments: Bio::DOOP::DBSQL object, promoter type (500, 1000, 3000), subset type (depends on reference species),
listref of clusters, temp file name (default: /tmp/fuzznuc_run.txt).
new_by_file
Create new fuzznuc object from query file.
Arguments: Bio::DOOP::DBSQL object, promoter type (500, 1000, 3000), subset type (depends on reference species),
file that contain cluster ids, temp file name (default: /tmp/fuzznuc_run.txt).
new_by_tmp
Create new Fuzznuc object from existing tmp file. It is good for
speed up the search with previously created tmp file.
Arguments: DBSQL object, tmp filename.
get_tmp_file_name
Get the temporary file name.
Return type: string
get_emboss_version
Get the installed emboss version number
$fuzznuc->get_emboss_version
run
Run mofext on temporary file, containing motifs.
Arguments: query pattern, mismatch, complement (0 or 1).
Return type: 0 -> success, -1 -> no result or error
run_background
Run fuzznuc, but don not wait for the end
Arguents: query pattern, mismatch, complement, output file name
Return type: the process id
get_results
Returns an arrayref of arrays of cluster objects.
get_results_from_file
Returns ... or -1 in case
of error.
This is a very uniq methods 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.