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    : 

cpanm Bio::DB::ESoap

perl -MCPAN -e shell
install Bio::DB::ESoap