Bio::Tools::Run::ERPIN.3pm

Langue: en

Autres versions - même langue

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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 => 'D-umask 4 D-add 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://bugzilla.open-bio.org/
 
 

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    :