Author image Endre Sebestyen
and 1 contributors

NAME

Bio::DOOP::Util::Run::Fuzznuc - Fuzznuc module

VERSION

Version 0.7

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 for patterns in the promoter sequences.

AUTHORS

Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary

METHODS

new

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');

new_by_file

Create new fuzznuc object from query file, containing cluster ids.

Arguments:

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');

new_by_tmp

Create new fuzznuc object from existing temporary file, containing query sequences in fasta format.

Arguments:

1. Bio::DOOP::DBSQL object 2. file containing fasta sequences

  $fuzznuc = Bio::DOOP::Util::Run::Fuzznuc->new($db,'/tmp/sequences.fasta');

get_tmp_file_name

Get the temporary file name.

   $tempname = $fuzznuc->get_tmp_file_name;

get_emboss_version

Get the installed emboss version.

   $version = $fuzznuc->get_emboss_version;

run

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');

run_background

Runs fuzznuc in background, returns the process id.

Arguments :

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');

get_raw_results

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};

get_results

Returns an arrayref of arrays with sequence objects and other information of the results.

The results contain the following:

1. Bio::DOOP::Sequence object 2. hit start 3. hit end 4. mismatch number 5. hit sequence 6. hit strand

   @result = @{$fuzznuc->get_raw_results};

get_results_from_file

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.

The results contain the following:

1. Bio::DOOP::Sequence object 2. hit start 3. hit end 4. mismatch number 5. hit sequence 6. hit strand

   @result = @{$fuzznuc->get_results_from_file};