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Summary

Bio::Tools::Run::Alignment::Pal2Nal - Wrapper for Pal2Nal

Package variables

Included modules

Inherit

Bio::Tools::Run::Phylo::PhyloBase

Synopsis

  use Bio::Tools::Run::Alignment::Pal2Nal;

  # Make a Pal2Nal factory
  $factory = Bio::Tools::Run::Alignment::Pal2Nal->new();

  # Run Pal2Nal with a protein alignment file and a multi-fasta nucleotide
  # file
  my $aln = $factory->run($protein_alignfilename, $nucleotide_filename);

  # or with Bioperl objects
  $aln = $factory->run($protein_bio_simplalign, [$nucleotide_bio_seq1,
                                                 $nucleotide_bio_seq2]);

  # combinations of files/ objects are possible

  # $aln isa Bio::SimpleAlign of the nucleotide sequences aligned according to
  # the protein alignment

Description

This is a wrapper for running the Pal2Nal perl script by Mikita Suyama. You
can get details here: http://coot.embl.de/pal2nal/. Pal2Nal is used for aligning
a set of nucleotide sequences based on an alignment of their translations.
You can try supplying normal pal2nal command-line arguments to new(), eg.
new() or calling arg-named methods (excluding the initial hyphen, eg.
$factory->(1) to set the - arg).
You will need to enable this Pal2Nal wrapper to find the pal2nal.pl script.
This can be done in (at least) three ways:

 1. Make sure the script is in your path.
 2. Define an environmental variable PAL2NALDIR which is a 
    directory which contains the script:
    In bash:

    export PAL2NALDIR=/home/username/pal2nal/

    In csh/tcsh:

    setenv PAL2NALDIR /home/username/pal2nal

 3. Include a definition of an environmental variable PAL2NALDIR in
    every script that will use this Pal2Nal wrapper module, e.g.:

    BEGIN { $ENV{PAL2NALDIR} = '/home/username/pal2nal/' }
    use Bio::Tools::Run::Alignment::Pal2Nal;

Methods

Methods description

 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns : string
 Args    : None

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns : string
 Args    : None

 Title   : new
 Usage   : $factory = Bio::Tools::Run::Alignment::Pal2Nal->new()
 Function: creates a new Pal2Nal factory.
 Returns : Bio::Tools::Run::Alignment::Pal2Nal
 Args    : Most options understood by pal2nal.pl can be supplied as key =>
           value pairs.

           These options can NOT be used with this wrapper:
           -output
           -html
           -h
           -nostderr

 Title   : run
 Usage   : $result = $factory->run($protein_align_file, $multi_fasta_nucleotide);
           -or-
           $result = $factory->run($prot_align_object, [$bioseq_object1, ...]);
 Function: Runs pal2nal on a protein alignment and set of nucleotide sequences.
 Returns : Bio::SimpleAlign;
 Args    : The first argument represents a protein alignment, the second
           argument a set of nucleotide sequences.
           The alignment can be provided as an alignment file readable by
           Bio::AlignIO, or a Bio::Align::AlignI compliant object (eg. a
           Bio::SimpleAlign).
           The nucleotide sequences can be provided as a single filename of a
           fasta file containing multiple nucleotide sequences, or an array ref
           of filenames, each file containing one sequence. Alternatively, an
           array ref of Bio::PrimarySeqI compliant objects can be supplied.
           
           In all cases, the protein alignment sequence names must correspond to
           the names of the supplied nucleotide sequences.

 Title   : _setparams
 Usage   : Internal function, not to be called directly
 Function: Creates a string of params to be used in the command string
 Returns : string of params
 Args    : alignment and tree file names

Methods code

sub program_name {

    return $PROGRAM_NAME;

}

sub program_dir {

    return $PROGRAM_DIR;

}

sub new {

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    $self->_set_from_args(\@args, -methods => [@PARAMS, @SWITCHES, 'quiet'],
                                  -create => 1);
    
    return $self;

}

sub run {

    my ($self, $aln, $nucs) = @_;
    
    ($aln && $nucs) || $self->throw("alignment and nucleotides must be supplied");
    $aln = $self->_alignment($aln);
    
    # gaps must be -, not .
    my $fixed_aln = Bio::SimpleAlign->new();
    foreach my $seq ($aln->each_seq) {
        my $str = $seq->seq;
        $str =~ s/\./-/g;
        $fixed_aln->add_seq(Bio::LocatableSeq->new(-id => $seq->id, -seq => $str));
    }
    $self->_alignment($fixed_aln);
    
    my $nucs_file;
    if (-e $nucs) {
        $nucs_file = $nucs;
    }
    elsif (ref($nucs) eq 'ARRAY') {
        (my $tempfh, $nucs_file) = $self->io->tempfile('-dir' => $self->tempdir(), UNLINK => ($self->save_tempfiles ? 0 : 1));
        close($tempfh);
        my $sout = Bio::SeqIO->new(-file => ">".$nucs_file, -format => 'fasta');
        
        foreach my $nuc (@{$nucs}) {
            if (-e $nuc) {
                my $sin = Bio::SeqIO->new(-file => $nuc);
                while (my $nuc_seq = $sin->next_seq) {
                    $sout->write_seq($nuc_seq);
                }
            }
            elsif (ref($nuc) && $nuc->isa('Bio::PrimarySeqI')) {
                $sout->write_seq($nuc);
            }
            else {
                $self->throw("Don't understand nucleotide argument '$nuc'");
            }
        }
    }
    else {
        $self->throw("Don't understand nucleotide argument '$nucs'");
    }
    
    return $self->_run($nucs_file);

}

sub _run {

    my ($self, $nucs_file) = @_;
    
    my $exe = $self->executable || return;
    
    my $aln_file = $self->_write_alignment;
    
    my ($rfh, $result_file) = $self->io->tempfile('-dir' => $self->tempdir(), UNLINK => ($self->save_tempfiles ? 0 : 1));
    my ($efh, $error_file) = $self->io->tempfile('-dir' => $self->tempdir(), UNLINK => ($self->save_tempfiles ? 0 : 1));
    close($rfh);
    undef $rfh;
    close($efh);
    undef $efh;
    my $command = $exe.$self->_setparams($aln_file, $nucs_file, $result_file, $error_file);
    $self->debug("pal2nal command = $command\n");
    
    system($command) && $self->throw("pal2nal call ($command) failed: $! | $?");
    open(my $errfh, '<', $error_file);
    my $errors;
    while (<$errfh>) {
        $errors .= $_;
    }
    close($errfh);
    $self->throw("pal2nal call ($command) had errors:\n$errors") if $errors;
    
    my $ain = Bio::AlignIO->new(-file => $result_file, -format => 'fasta');
    my $aln = $ain->next_aln;
    $ain->close;
    
    return $aln;

}

sub _setparams {

    my ($self, $aln_file, $nucs_file, $result_file, $error_file) = @_;
    
    my $param_string = ' '.$aln_file;
    $param_string .= ' '.$nucs_file;
    $param_string .= $self->SUPER::_setparams(-params =>\@ PARAMS,
                                              -switches =>\@ SWITCHES,
                                              -dash => 1);
    $param_string .= ' -output fasta';
    
    $param_string .= " > $result_file 2> $error_file";
    
    return $param_string;
}

1;

}

General documentation

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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _