Bio::DOOP::Util::Run::Mofext - Mofext runner module.
Version 0.16
#!/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}; # Return the motif objects and the score, extended score. for $result (@res){ print $$result[0]->get_id," ",$$result[1],"$$result[2]","\n"; }
Mofext is a fuzzy sequence pattern search tool developed by Tibor Nagy. This module is a wrapper object for mofext. It allows the user to search for similar motifs in the DOOP database.
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
Create a new Mofext object. Arguments: DBSQL object, promoter type (500,1000,3000), subset type (B,M,E,V in plants) arrayref of cluster ids.
Create a new Mofext object from a file. Arguments: DBSQL object, promoter type (500, 1000, 3000), subset type (B,M,E,V in plants), name of the file with cluster ids.
Create a new Mofext object from a existing tmp file. It is useful when you have a tmp file, and you want to use it over and over, or your tmp file is large (the new constructor is very slow when you use large cluster lists). If you use this constructor, you don't need to use set_tmp_file_name and write_to_tmp. Arguments: Bio::DOOP::DBSQL object, temporary file name. Return type: none Example: use Bio::DOOP::DOOP $db = Bio::DOOP::DBSQL->connect("username","pswd","doop-chordate-1_4","localhost"); $mofext = Bio::DOOP::Util::Run::Mofext->new_by_tmp($db,"/adatok/prg/perl/DOOP/ize.txt"); $ret = $mofext->run('GGATCCTGGAT',10,0.95,'default_matrix.txt'); @res = @{$mofext->get_results}; for $res (@res){ print $$res[0]->get_id," ",$$res[1],"\n"; }
Get the temporary file name. Return type: string
Set the temporary file name. Arguments: 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 do not wait for it to finish. Arguments: query sequence, wordsize, cutoff, matrix file path, output file name. Return type: the process id
Returns the arrayref of array of motif objects and score, extended score, full hit sequence, alignment start position in the query sequence, alignment start position in the hit sequence.
Returns the arrayref of the array of motif objects and anything else like the get_results method or -1 in the case of an 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.
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.