NAME
Bio::DOOP::Util::Run::Fuzznuc - Fuzznuc runner module.
VERSION
Version 0.5
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");
$fuzznuc = Bio::DOOP::Util::Run::Fuzznuc->new($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 with it.
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
Creates 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
Creates new Fuzznuc object from existing tmp file. It is good for
speeding up the search with a previously created tmp file.
Arguments: DBSQL object, tmp filename.
get_tmp_file_name
Get the temporary file name.
Return type: string
get_emboss_version
$fuzznuc->get_emboss_version
Get the installed emboss version number
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 do not wait for the search to finish.
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 method because it does not depend on the object. So you can fetch
different results of different mofext objects.