/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Alignment::Exonerate

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.

PROGRAM VERSIONS

The tests have been shown to pass with exonorate versions 2.0 - 2.2.

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 - 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    :