Bio::DOOP::Util::Run::Fuzznuc - Fuzznuc module
Version 0.7
#!/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 for patterns in the promoter sequences.
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
Create new Fuzznuc object.
Arguments:
1. Bio::DOOP::DBSQL object 2. promoter type (500, 1000, 3000) 3. subset type (depends on reference species) 4. arrayref of clusters 5. temporary file name (default: /tmp/fuzznuc_run.txt, will contain fasta sequences)
$fuzznuc = Bio::DOOP::Util::Run::Fuzznuc->new($db,500,'M',\@list,'/tmp/tmpfile');
Create new fuzznuc object from query file, containing cluster ids.
1. Bio::DOOP::DBSQL object 2. promoter type (500, 1000, 3000) 3. subset type (depends on reference species) 4. file containing cluster ids 5. temporary file name (default: /tmp/fuzznuc_run.txt, will contain fasta sequences)
$fuzznuc = Bio::DOOP::Util::Run::Fuzznuc->new($db,500,'M','/tmp/clusters.txt','/tmp/tmpfile');
Create new fuzznuc object from existing temporary file, containing query sequences in fasta format.
1. Bio::DOOP::DBSQL object 2. file containing fasta sequences
$fuzznuc = Bio::DOOP::Util::Run::Fuzznuc->new($db,'/tmp/sequences.fasta');
Get the temporary file name.
$tempname = $fuzznuc->get_tmp_file_name;
Get the installed emboss version.
$version = $fuzznuc->get_emboss_version;
Runs fuzznuc, returns 0 on success, otherwise -1.
Arguments :
1. query pattern 2. mismatch number 3. complement (0 or 1)
$fuzznuc_error = $fuzznuc->run('AACCAGGTT','1','1');
Runs fuzznuc in background, returns the process id.
1. query pattern 2. mismatch number 3. complement (0 or 1) 4. output filename
$fuzznuc_pid = $fuzznuc->run_background('AACCAGGTT','1','1','/tmp/fuzznuc_result.txt');
Returns an arrayref of arrays with the raw fuzznuc results, without Bio::DOOP objects. This is much faster as it does not use the database.
The results contain the following:
1. sequence ID 2. hit start 3. hit end 4. mismatch number 5. hit sequence 6. hit strand
@result = @{$fuzznuc->get_raw_results};
Returns an arrayref of arrays with sequence objects and other information of the results.
1. Bio::DOOP::Sequence object 2. hit start 3. hit end 4. mismatch number 5. hit sequence 6. hit strand
Returns an arrayref of arrays with sequence objects and other information of the results from a results file. With this method you can fetch the results of different fuzznuc objects.
@result = @{$fuzznuc->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.