NAME

Bio::Tools::Run::Alignment::Exonerate

SYNOPSIS

  use Bio::Tools::Run::Alignment::Exonerate;
  use Bio::SeqIO;

  my $qio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>'fasta');
  my $query = $qio->next_seq();
  my $tio = Bio::SeqIO->new(-file=>$ARGV[1],-format=>'fasta');
  my $target = $sio->next_seq();

  #exonerate parameters can all be passed via arguments parameter.
  #parameters passed are not checked for validity

  my $run = Bio::Tools::Run::Alignment::Exonerate->new(arguments=>'--model est2genome --bestn 10');
  my $searchio_obj = $run->run($query,$target);

  while(my $result = $searchio->next_result){
    while( my $hit = $result->next_hit ) {
      while( my $hsp = $hit->next_hsp ) {
        print $hsp->start."\t".$hsp->end."\n";
      }
    }
  }

DESCRIPTION

  Wrapper for Exonerate alignment program. You can get exonerate at
  http://www.ebi.ac.uk/~guy/exonerate/.
  This wrapper is written without parameter checking. All parameters are passed
  via the arugment parameter that is passed in the constructor. See SYNOPSIS.
  For exonerate parameters, run exonerate --help for more details.

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

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 - Shawn Hoon

  Email shawnh-at-stanford.edu

APPENDIX

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

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, obtiained from ENV variable.
 Returns:  string
 Args    :

new

 Title   : new
 Usage   : my $factory= Bio::Tools::Run::Phrap->new();
 Function: creates a new Phrap factory
 Returns:  Bio::Tools::Run::Phrap
 Args    :

run

 Title   :   run()
 Usage   :   my $feats = $factory->run($seq)
 Function:   Runs Phrap 
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :   A Bio::PrimarySeqI

_input

 Title   :   _input
 Usage   :   $factory->_input($seqFile)
 Function:   get/set for input file
 Returns :
 Args    :

_run

 Title   :   _run
 Usage   :   $factory->_run()
 Function:   Makes a system call and runs Phrap
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :

_writeInput

 Title   :   _writeInput
 Usage   :   $factory->_writeInput($query,$target)
 Function:   Creates a file from the given seq object
 Returns :   A string(filename)
 Args    :   Bio::PrimarySeqI

_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    :

CPAN RT