Bio::DOOP::Util::Run::Fuzznuc - Fuzznuc runner module.
Version 0.4
#!/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");
$fuzznuc = Bio::DOOP::Util::Run::Fuzznuc->new($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"; }
This module is a wrapper for the EMBOSS (http://emboss.sourceforge.net) program fuzznuc. You can search patterns in the promoter sequences.
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
$fuzznuc = Bio::DOOP::Util::Run::Fuzznuc->new($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) arrayref of clusters temporary file name (default: /tmp/fuzznuc_run.txt)
Create new fuzznuc object from query file, containing cluster ids. Arguments : Bio::DOOP::DBSQL object promoter type (500, 1000, 3000) subset type (depends on reference species) file that contain cluster ids temporary file name (default: /tmp/fuzznuc_run.txt)
Create new Fuzznuc object from existing temporary file, containing query sequences in fasta format. Arguments : DBSQL object temporary file name
Get the temporary file name. Return type : string
Get the installed emboss version number. $fuzznuc->get_emboss_version Return type : string
Run fuzznuc on temporary file, containing sequences. Arguments : query pattern mismatch number complement (0 or 1) Return type : 0 if success, -1 if no results or error happened
Run fuzznuc, but do not wait for completion. Arguments : query pattern mismatch number complement (0 or 1) output filename Return type : process id
Returns an arrayref of arrays of the raw fuzznuc result without objects. It is much faster because does not use the database.
Returns an arrayref of arrays of sequence objects.
Returns an arrayref of arrays of sequence objects or -1 if an error happened. This is a very unique methods because it does not depend on the object. With it you can fetch the results of different fuzznuc objects. Maybe it will go out from the 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.