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# Wrapper  module for Exonerate Bio::Tools::Run::Alignment::Exonerate
# $Id: Exonerate.pm 15564 2009-02-24 01:59:09Z cjfields $
# 
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Shawn Hoon
#
# Copyright Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
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=head1 NAME
Bio::Tools::Run::Alignment::Exonerate
=head1 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";
      }
    }
  }
=head1 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.
=head1 FEEDBACK
=head2 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
=head2 Support 
  
Please direct usage questions or support issues to the mailing list:
   
L<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.
=head2 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/
=head1 AUTHOR - Shawn Hoon
  Email shawnh-at-stanford.edu
=head1 APPENDIX
 The rest of the documentation details each of the object
 methods. Internal methods are usually preceded with a _
=cut
package Bio::Tools::Run::Alignment::Exonerate;
use vars qw($AUTOLOAD @ISA $PROGRAM  $PROGRAMDIR
            $PROGRAMNAME @EXONERATE_PARAMS %OK_FIELD);
use strict;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Factory::ApplicationFactoryI;
use Bio::Tools::Run::WrapperBase;
use Bio::SearchIO;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase 
          Bio::Factory::ApplicationFactoryI);
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=head2 program_name
 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns:  string
 Args    : None
=cut
sub program_name {
    return 'exonerate';
}
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=head2 program_dir
 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns:  string
 Args    :
=cut
sub program_dir {
    return Bio::Root::IO->catfile($ENV{EXONERATEDIR}) if $ENV{EXONERATEDIR};
}
sub AUTOLOAD {
       my $self = shift;
       my $attr = $AUTOLOAD;
       $attr =~ s/.*:://;
       $attr = uc $attr;
       $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
       $self->{$attr} = shift if @_;
       return $self->{$attr};
}
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=head2 new
 Title   : new
 Usage   : my $factory= Bio::Tools::Run::Phrap->new();
 Function: creates a new Phrap factory
 Returns:  Bio::Tools::Run::Phrap
 Args    :
=cut
sub new {
       my ($class,@args) = @_;
       my $self = $class->SUPER::new(@args);
  
       my ($attr, $value);
       while (@args)  {
           $attr =   shift @args;
           $value =  shift @args;
           next if( $attr =~ /^-/ ); # don't want named parameters
           if ($attr =~/PROGRAM/i) {
              $self->executable($value);
              next;
           }
           $self->$attr($value);
       }
       return $self;
}
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=head2  version
 Title   : version
 Usage   : exit if $prog->version() < 1.8
 Function: Determine the version number of the program
 Example :
 Returns : float or undef
 Args    : none
=cut
sub version {
    my ($self) = @_;
    my $exe;
    return undef unless $exe = $self->executable;
    my $string = `$exe -v` ;
    #exonerate from exonerate version 2.0.0\n...
    my ($version) = $string =~ /exonerate version ([\d+\.]+)/m;
    $version =~ s/\.(\d+)$/$1/;
    return $version || undef;
}
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=head2 run
 Title   :   run()
 Usage   :   my $feats = $factory->run($seq)
 Function:   Runs Phrap 
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :   A Bio::PrimarySeqI
=cut
sub run {
    my ($self,$query,$target) = @_;
    my @feats;
    my ($file1) = $self->_writeInput($query);
    my ($file2) = $self->_writeInput($target);    
    my $assembly = $self->_run($file1,$file2);
    return $assembly;
}
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=head2 _input
 Title   :   _input
 Usage   :   $factory->_input($seqFile)
 Function:   get/set for input file
 Returns :
 Args    :
=cut
sub _input() {
     my ($self,$infile1) = @_;
     $self->{'input'} = $infile1 if(defined $infile1);
     return $self->{'input'};
 }
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=head2 _run
 Title   :   _run
 Usage   :   $factory->_run()
 Function:   Makes a system call and runs Phrap
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :
=cut
sub _run {
     my ($self,$query,$target)= @_;
     my ($tfh,$outfile) = $self->io->tempfile(-dir=>$self->tempdir);
     my $param_str = $self->_setparams." ".$self->arguments;
     my $str = $self->executable." $param_str $query $target "." > $outfile";
     $self->debug( "$str\n");
     my $status = system($str);
     $self->throw( "Exonerate call ($str) crashed: $? \n") unless $status==0;
     my $filehandle;
     my $exonerate_obj = Bio::SearchIO->new(-file=>"$outfile",-format=>'exonerate');
     close($tfh);
     undef $tfh;    
     unlink $outfile;
      
     return $exonerate_obj;
}
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=head2 _writeInput
 Title   :   _writeInput
 Usage   :   $factory->_writeInput($query,$target)
 Function:   Creates a file from the given seq object
 Returns :   A string(filename)
 Args    :   Bio::PrimarySeqI
=cut
sub _writeInput{
    my ($self,$query) = @_;
    my ($fh,$infile1);
    if (ref($query) =~ /ARRAY/i) {
      my @infilearr;
      ($fh, $infile1) = $self->io->tempfile();
      my $temp = Bio::SeqIO->new( -file => ">$infile1",
                                  -format => 'Fasta' );
      foreach my $seq1 (@$query) {
        unless ($seq1->isa("Bio::PrimarySeqI")) {
          return 0;
        }
        $temp->write_seq($seq1);
        push @infilearr, $infile1;
      }
    }
    elsif($query->isa("Bio::PrimarySeqI")) {
      ($fh, $infile1) = $self->io->tempfile();
      my $temp = Bio::SeqIO->new( -file => ">$infile1",
                                  -format => 'Fasta' );
      $temp->write_seq($query);
    }
    else {
      $infile1 = $query;
    }
    return $infile1;
}
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=head2 _setparams
 Title   :  _setparams
 Usage   :  Internal function, not to be called directly
 Function:  creates a string of params to be used in the command string
 Example :
 Returns :  string of params
 Args    :  
=cut
sub _setparams {
    my ($self) = @_;
    my $param_string = '';
    foreach my $attr(@EXONERATE_PARAMS){
        next if($attr=~/PROGRAM/);
        my $value = $self->$attr();
        next unless (defined $value);
        my $attr_key = ' -'.(lc $attr);
        $param_string .= $attr_key.' '.$value;
    }
    return $param_string;
}
1;