Bio::DOOP::Util::Run::Mofext - Mofext module
Version 0.17
#!/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}; # Returns the motif objects, score and 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 new Mofext object.
Arguments:
1. Bio::DOOP::DBSQL object 2. promoter type (500, 1000, 3000) 3. subset type (depends on reference species) 4. arrayref of cluster ids
$mofext = Bio::DOOP::Util::Run::Mofext->new($db,500,'B',\@list);
Create a new Mofext object from query file, containing cluster ids, one per line.
1. Bio::DOOP::DBSQL object 2. promoter type (500, 1000, 3000) 3. subset type (depends on reference species) 4. name of file with cluster ids
$mofext = Bio::DOOP::Util::Run::Mofext->new_by_file($db,500,'B','/tmp/clusters.txt');
Create a new Mofext object from an existing temporary file containing conserved motifs. It is useful in some cases, because the new constructor is very slow when you use large cluster lists. If you use this constructor, you don't need to use the set_tmp_file_name and write_to_tmp methods.
1. Bio::DOOP::DBSQL object 2. temporary file name
$mofext = Bio::DOOP::Util::Run::Mofext->new_by_tmp($db,"/tmp/motifs.txt");
Get the name of the temporary file containing the motifs.
$tmp_name = $mofext->get_tmp_file_name;
Set the temporary file name.
$mofext->set_tmp_file_name('/tmp/motifs.txt');
Write out the collected motifs to the temporary file.
$write_error = $mofext->write_to_tmp;
Runs mofext, returns 0 on success, otherwise -1.
1. query sequence 2. wordsize 3. cutoff 4. matrix file path/name
A typical matrix looks like this:
11 A T G C S W R Y K M N A 5 -4 -4 -4 -4 1 1 -4 -4 1 -2 T -4 5 -4 -4 -4 1 -4 1 1 -4 -2 G -4 -4 5 -4 1 -4 1 -4 1 -4 -2 C -4 -4 -4 5 1 -4 -4 1 -4 1 -2 S -4 -4 1 1 -1 -4 -2 -2 -2 -2 -1 W 1 1 -4 -4 -4 -1 -2 -2 -2 -2 -1 R 1 -4 1 -4 -2 -2 -1 -4 -2 -2 -1 Y -4 1 -4 1 -2 -2 -4 -1 -2 -2 -1 K -4 1 1 -4 -2 -2 -2 -2 -1 -4 -1 M 1 -4 -4 1 -2 -2 -2 -2 -4 -1 -1 N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1
$mofext_error = $mofext->run('AAGTKSAAT','7','90','/data/run/matrix.txt')
Runs mofext in background, returns the process id.
1. query sequence 2. wordsize 3. cutoff 4. matrix file path/name 5. output file path/name
$mofext_pid = $mofext->run_background('AAGTKSAAT','7','90','/data/run/matrix.txt','/data/run/mofext_results.txt');
Returns an arrayref of arrays with motif objects and other information of the results.
The results contain the following:
1. Bio::DOOP::Motif object 2. motif score 3. motif extended score 4. full hit sequence 5. alignment start position in the query sequence 6. alignment start position in the hit sequence
@result = @{$mofext->get_results};
Returns an arrayref of arrays with motif objects and other information of the results from a results file. With this method you can fetch the results of different mofext objects.
@result = @{$mofext->get_results_from_file};
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.