NAME

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

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;

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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:

  http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala

Email bix@sendu.me.uk

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    : None

new

 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

run

 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.

_setparams

 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