Christopher Fields > BioPerl-Run > Bio::Tools::Run::ERPIN

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BioPerl-Run-1.006900.tar.gz

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NAME ^

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

SYNOPSIS ^

  #run 

  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],
                            'nomask',
                            'cutoff'  => [0, 10, 15, 20]
                            ]
              # or use a simple string...
              #strategy => 'Ðumask 4 Ðadd 5 -nomask -cutoff 0 10 15',
              pcw => 100
             );

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

  # 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,
                               $hit->name,
                               $hsp->hit->start,
                               $hsp->hit->end,
                               $hsp->meta,
                               $hsp->score,
                               )), "\n";
    }
   }
  }

DESCRIPTION ^

FEEDBACK ^

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Chris Fields ^

 Email: cjfields-at-uiuc-dot-edu

CONTRIBUTORS ^

 cjfields-at-uiuc-dot-edu

APPENDIX ^

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

new

 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)

program_name

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

program_dir

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

version

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

run

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

tempfile

 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

_run

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

_setparams

 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    :  

_writeSeqFile

 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    : 
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