Bio::Tools::Run::Alignment::Exonerate.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

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
 
 

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 - 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, obtained 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    :
 
 

version

  Title   : version
  Usage   : exit if $prog->version() < 1.8
  Function: Determine the version number of the program
  Example :
  Returns : float or undef
  Args    : none
 
 

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    :