Bio::DOOP::Util::Run::Fuzznuc - Fuzznuc runner module.
Version 0.2
#!/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);
$fuzznuc->set_tmp_file_name("/data/DOOP/dummy.txt");
print $fuzznuc->get_tmp_file_name,"\n";
$error = $fuzznuc->write_to_tmp;
if($error != 0){ die "Write error!\n"; }
$error = $fuzznuc->run('TTGGGC' , 6 , 0.6 , '/data/default_matrix' );
if ($error == -1){ die "No results or error!\n"; }
@res = @{$fuzznuc->get_results};
This module is a wrapper for the Emboss program fuzznuc. You can search patterns in the promoter sequences.
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
Create new fuzznuc object from query file.
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 the temporary file name. Return type: string
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 fuzznuc, but don not wait for the end Arguents: query pattern, mismatch, complement, output file name Return type: the process id
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.
To install Bio::DOOP::DOOP, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DOOP::DOOP
CPAN shell
perl -MCPAN -e shell install Bio::DOOP::DOOP
For more information on module installation, please visit the detailed CPAN module installation guide.