Bio::DOOP::Util::Run::Mofext - Mofext runner module.
Version 0.09
#!/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");
$mofext = Bio::DOOP::Util::Run::Mofext->new($db,'500',\@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}; # Return the cluster objects and the motif primary ids. for $result (@res){ print $$result[0]->get_id," ",$$result[1],"\n"; }
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.
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
Create a new Mofext object. Arguments: DBSQL object, promoter type (500,1000,3000), arrayref of cluster ids.
Create a new Mofext object from a file. Arguments: DBSQL object, promoter type (500, 1000, 3000), name of the file with cluster ids.
Get the temporary file name. Return type: string
Set the temporary file name. Return type: none
Write out the collected motifs to the temporary file. Return type: 0 -> success, -1 -> error
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 mofext, but don not wait for the end Arguents: query sequence, wordsize, cutoff, matrix file path, output file name Return type: the process id
Returns the arrayref of array of cluster objects and motif primary ids.
Returns the arrayref of the array of cluster objects and motif primary ids 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.