Provided by: libbio-perl-run-perl_1.7.1-3_all bug


       Bio::Tools::Run::ERPIN - Wrapper for local execution of the ERPIN suite of programs.



         my @params = (
                     trset => 'BL.erpin',
                     region => [1, 10],
                     # Set up search strategy this way...
                     strategy => [ 'umask'   => [1, 2],
                                   'umask'   => [1, 2, 3, 4],
                                   'umask'   => [1, 2, 3, 4, 5, 6],
                                   'cutoff'  => [0, 10, 15, 20]
                     # or use a simple string...
                     #strategy => '‐umask 4 ‐add 5 -nomask -cutoff 0 10 15',
                     pcw => 100

         my $factory = Bio::Tools::Run::ERPIN->new(-program =>'erpin',

         # Pass the factory a Bio::Seq object or a file name
         # Returns a Bio::SearchIO object

         #my $search = $factory->run("B_sub.fas");
         my $search = $factory->run($seq);
         my @feat;
         while (my $result = $searchio->next_result){
          while(my $hit = $result->next_hit){
           while (my $hsp = $hit->next_hsp){
                   print join("\t", ( $r->query_name,
                                      )), "\n";



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AUTHOR - Chris Fields

        Email: cjfields-at-uiuc-dot-edu




       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : my $wrapper = Bio::Tools::Run::RNAMotif->new(@params)
        Function: creates a new RNAMotif factory
        Returns:  Bio::Tools::Run::RNAMotif
        Args    : list of parameters
                  -tempfile        => set tempfile flag (default 0)
                  -outfile_name    => set file to send output to (default none)

        Title   : program_name
        Usage   : $factory>program_name()
        Function: holds the program name
        Returns:  string
        Args    : None

        Title   : program_dir
        Usage   : $factory->program_dir(@params)
        Function: returns the program directory, obtained from ENV variable.
        Returns:  string
        Args    :

        Title   : version
        Usage   : $v = $prog->version();
        Function: Determine the version number of the program
        Example :
        Returns : float or undef
        Args    : none

        Title   :  run
        Usage   :  $obj->run($seqFile)
        Function:  Runs ERPIN programs and returns Bio::SearchIO
        Returns :
        Args    :  Must pass Bio::PrimarySeqI's or file names

        Title   : tempfile
        Usage   : $obj->tempfile(1)
        Function: Set tempfile flag.  When set, writes output to a tempfile; this
                  is overridden by outfile_name() if set
        Returns : Boolean setting (or undef if not set)
        Args    : [OPTIONAL] Boolean

        Title   :   _run
        Usage   :   $obj->_run()
        Function:   Internal(not to be used directly)
        Returns :
        Args    :

        Title   :  _setparams
        Usage   :  Internal function, not to be called directly
        Function:  creates a string of params to be used in the command string
        Example :
        Returns :  string of params
        Args    :

        Title   : _writeSeqFile
        Usage   : obj->_writeSeqFile($seq)
        Function: Internal(not to be used directly)
        Returns : writes passed Seq objects to tempfile, to be used as input
                  for program
        Args    :


       Hey! The above document had some coding errors, which are explained below:

       Around line 34:
           Non-ASCII character seen before =encoding in ''‐umask'. Assuming CP1252