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#
#
#  Copyright Balamurugan Kumarasamy
#
#  You may distribute this module under the same terms as perl itself
#  POD documentation - main docs before the code
#
HideShow 58 lines of Pod
=head1 NAME
Bio::Tools::Run::Tmhmm - Object for identifying transmembrane helixes
  in a given protein seequence.
=head1 SYNOPSIS
  # Build a Tmhmm  factory
  # $paramfile is the full path to the seg binary file
  my @params = ('PROGRAM',$paramfile);
  my $factory = Bio::Tools::Run::Tmhmm->new($param);
  # Pass the factory a Bio::Seq object
  # @feats is an array of Bio::SeqFeature::Generic objects
  my @feats = $factory->run($seq);
=head1 DESCRIPTION
Tmhmm is a program for identifying transmembrane helices in proteins.
You must have the environmental variable TMHMMDIR set to the base
directory where I<tmhmm> and it's associated data/option files reside
(NOT the bin directory where the actual executable resides)
=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 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/
=head1 AUTHOR - Bala
 Email savikalpa@fugu-sg.org
=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::Tmhmm;
use vars qw($AUTOLOAD @ISA $PROGRAMNAME @TMHMM_PARAMS %OK_FIELD);
use strict;
use Cwd;
use Bio::SeqIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Tools::Tmhmm;
use Bio::Tools::Run::WrapperBase;
@ISA = qw(Bio::Tools::Run::WrapperBase);
BEGIN {
    $PROGRAMNAME = 'tmhmm'  . ($^O =~ /mswin/i ?'.exe':'');       
    @TMHMM_PARAMS=qw(PROGRAM VERBOSE NOPLOT);
    foreach my $attr ( @TMHMM_PARAMS)
    { $OK_FIELD{$attr}++; }
}
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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 $PROGRAMNAME;
}
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=head2 program_dir
 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable, in this
           case it is the tmhmm installation directory, not the location of
           the executable.
 Returns:  string
 Args    :
=cut
sub program_dir {
    return $ENV{TMHMMDIR} || '';
}
HideShow 10 lines of Pod
=head2 program_path
 Title   : program_path
 Usage   : my $path = $factory->program_path();
 Function: Builds path for executable 
 Returns : string representing the full path to the exe
 Args    : none
=cut
sub program_path {
    my ($self) = @_;
    my @path;
    if ($self->program_dir) {
        my $program_dir = $self->program_dir;
        $program_dir =~ s/\/bin//;
        push @path, $program_dir;
    }
    push @path, 'bin';
    push @path, $self->program_name.($^O =~ /mswin/i ?'.exe':'');
    return File::Spec->catfile(@path);
}
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};
}
HideShow 10 lines of Pod
=head2 new
 Title   : new
 Usage   : $rm->new(@params)
 Function: creates a new Tmhmm factory
 Returns:  Bio::Tools::Run::Tmhmm
 Args    :
=cut
sub new {
       my ($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
           $self->$attr($value);
       }
       return $self;
}
HideShow 10 lines of Pod
=head2 predict_protein_features
 Title   :   predict_protein_features()
 Usage   :   DEPRECATED Use $obj->run($seq) instead
 Function:   Runs Tmhmm and creates an array of featrues
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :   A Bio::PrimarySeqI
=cut
sub predict_protein_features{
        return shift->run(@_);
}
HideShow 11 lines of Pod
=head2 executable
 Title   : executable
 Usage   : my $exe = $tmhmm->executable('tmhmm');
 Function: Finds the full path to the 'tmhmm' executable
 Returns : string representing the full path to the exe
 Args    : [optional] name of executable to set path to
           [optional] boolean flag whether or not warn when exe is not found
=cut
sub executable {
    my $self = shift;
    my $exe = $self->SUPER::executable(@_) || return;
     
    # even if its executable, we still need the environment variable to have
    # been set
    if (! $ENV{TMHMMDIR}) {
        $self->warn("Environment variable TMHMMDIR must be set, even if the tmhmm executable is in your path");
        return undef;
    }
     
    return $exe;
}
HideShow 10 lines of Pod
=head2 run
 Title   :   run()
 Usage   :   $obj->run($seq)
 Function:   Runs Tmhmm and creates an array of featrues
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :   A Bio::PrimarySeqI
=cut
sub run {
    my ($self,$seq) = @_;
    my @feats;
    if (ref($seq) ) {           # it is an object
        if (ref($seq) =~ /GLOB/) {
            $self->throw("cannot use filehandle");
        }
        my $infile1 = $self->_writeSeqFile($seq);
        $self->_input($infile1);
        @feats = $self->_run();
        unlink $infile1;
    }
    else {
        # The clone object is not a seq object but a file.  Perhaps
        # should check here or before if this file is fasta format...if
        # not die Here the file does not need to be created or
        # deleted. Its already written and may be used by other
        # runnables.
        $self->_input($seq);
        @feats = $self->_run();
    }
    return @feats;
}
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=head2 _input
 Title   :   _input
 Usage   :   obj->_input($seqFile)
 Function:   Internal(not to be used directly)
 Returns :
 Args    :
=cut
sub _input() {
     my ($self,$infile1) = @_;
     if (defined $infile1){
         $self->{'input'}=$infile1;
     }
      return $self->{'input'};
}
HideShow 10 lines of Pod
=head2 _run
 Title   :   _run
 Usage   :   $obj->_run()
 Function:   Internal(not to be used directly)
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :
=cut
sub _run {
     my ($self)= @_;
     my ($tfh1,$outfile) = $self->io->tempfile(-dir=>$self->tempdir());
     my $str = $self->executable || return;
      
     if( $self->NOPLOT ) {
         $str .= " --noplot";
     }
     $str .= " -basedir=".$self->program_dir." -workdir=".$self->tempdir()." ".$self->_input." > ".$outfile;
      
     my $status = system($str);
     $self->throw( "Tmhmm call ($str) crashed: $? \n") unless $status==0;
     
     my $filehandle;
     if (ref ($outfile) !~ /GLOB/) {
        open (TMHMM, "<".$outfile) or $self->throw ("Couldn't open file ".$outfile.": $!\n");
        $filehandle = \*TMHMM;
     }
     else {
        $filehandle = $outfile;
     }
     my $tmhmm_parser = Bio::Tools::Tmhmm->new(-fh=>$filehandle);
     my @tmhmm_feat;
     while(my $tmhmm_feat = $tmhmm_parser->next_result){
           push @tmhmm_feat, $tmhmm_feat;
     }
     # free resources
     $self->cleanup();
     unlink $outfile;
     close($tfh1);
     undef $tfh1;
      
     return @tmhmm_feat;
}
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=head2 _writeSeqFile
 Title   :   _writeSeqFile
 Usage   :   obj->_writeSeqFile($seq)
 Function:   Internal(not to be used directly)
 Returns :
 Args    :
=cut
sub _writeSeqFile{
    my ($self,$seq) = @_;
    my ($tfh,$inputfile) = $self->io->tempfile(-dir=>$self->tempdir());
    my $in  = Bio::SeqIO->new(-fh => $tfh , '-format' => 'Fasta');
    $in->write_seq($seq);
    close($tfh);
    undef $tfh;
    return $inputfile;
}
1;