NAME
Bio::DOOP::Util::Run::Fuzznuc - Fuzznuc runner module.
VERSION
Version 0.4
SYNOPSIS
#!/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"; }
DESCRIPTION
This module is a wrapper for the EMBOSS (http://emboss.sourceforge.net) program fuzznuc. You can search
patterns in the promoter sequences.
AUTHORS
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
METHODS
new
$fuzznuc = Bio::DOOP::Util::Run::Fuzznuc->new($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)
new_by_file
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)
new_by_tmp
Create new Fuzznuc object from existing temporary file, containing query sequences in fasta format.
Arguments :
DBSQL object
temporary file name
get_tmp_file_name
Get the temporary file name.
Return type :
string
get_emboss_version
Get the installed emboss version number.
$fuzznuc->get_emboss_version
Return type :
string
run
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_background
Run fuzznuc, but do not wait for completion.
Arguments :
query pattern
mismatch number
complement (0 or 1)
output filename
Return type :
process id
get_raw_results
Returns an arrayref of arrays of the raw fuzznuc result without objects.
It is much faster because does not use the database.
get_results
Returns an arrayref of arrays of sequence objects.
get_results_from_file
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.