BioPerl-Run

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lib/Bio/Tools/Run/Alignment/Blat.pm  view on Meta::CPAN

#=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'};
}


#=head2 _database
#
# Title   : _database
# Usage   : obj->_database($seqFile)
# Function: Internal (not to be used directly)
# Returns :
# Args    :
#
#=cut

sub _database() {
    my ($self,$infile1) = @_;
    $self->{'db'} = $infile1 if(defined $infile1);
    return $self->{'db'};
}


#=head2 _run
#
# Title   : _run
# Usage   : $obj->_run()

lib/Bio/Tools/Run/Alignment/Exonerate.pm  view on Meta::CPAN

=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'};
 }

=head2 _run

 Title   :   _run
 Usage   :   $factory->_run()
 Function:   Makes a system call and runs Phrap

lib/Bio/Tools/Run/Coil.pm  view on Meta::CPAN

=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'};

}

=head2 _run

lib/Bio/Tools/Run/Genscan.pm  view on Meta::CPAN

=head2 _set_input()

    Title   :   _set_input
    Usage   :   obj->_set_input($matrixFile,$seqFile)
    Function:   Internal(not to be used directly)
    Returns :  
    Args    :

=cut

sub _set_input() {
   my ($self,$infile1) = @_;
   $self->{'input'}=$infile1;
}

=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);
  $in->close();
  close($tfh);
  undef $tfh;
  return $inputfile;
}

lib/Bio/Tools/Run/Prints.pm  view on Meta::CPAN

=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'};

}

lib/Bio/Tools/Run/Profile.pm  view on Meta::CPAN

=head2 _input

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

=cut

sub _input() {
     my ($self,$infile1) = @_;
     if(defined $infile1){
        $self->{'input'}=$infile1;
     }
      return $self->{'input'};
}

=head2 _run

 Title   :   _run

lib/Bio/Tools/Run/Signalp.pm  view on Meta::CPAN

=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'};
 }

=head2 _run

 Title   :   _run
 Usage   :   $factory->_run()
 Function:   Makes a system call and runs signalp

lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm  view on Meta::CPAN

=head2 next_result()

 Title   : next_result
 Usage   : $result = $fac->next_result;
 Function: get the next BLAST result
 Returns : Bio::Search::Result::BlastResult object
 Args    : none

=cut

sub next_result() {
    my $self = shift;
    return unless $self->{_results};
    return $self->{_results}->next_result;
}

=head2 rewind_results()

 Title   : rewind_results
 Usage   : $fac->rewind_results;
 Function: rewind BLAST results

lib/Bio/Tools/Run/Tmhmm.pm  view on Meta::CPAN

=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'};
}

=head2 _run