view release on metacpan or  search on metacpan

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

=pod

=encoding UTF-8

=head1 NAME

Bio::Tools::Run::Alignment::TCoffee - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program

=head1 VERSION

version 1.7.4

=head1 SYNOPSIS

  # Build a tcoffee alignment factory
  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
  $factory = Bio::Tools::Run::Alignment::TCoffee->new(@params);

  # Pass the factory a list of sequences to be aligned.
  $inputfilename = 't/cysprot.fa';
  # $aln is a SimpleAlign object.
  $aln = $factory->align($inputfilename);

  # or where @seq_array is an array of Bio::Seq objects
  $seq_array_ref = \@seq_array;
  $aln = $factory->align($seq_array_ref);

  # Or one can pass the factory a pair of (sub)alignments
  #to be aligned against each other, e.g.:

  # where $aln1 and $aln2 are Bio::SimpleAlign objects.
  $aln = $factory->profile_align($aln1,$aln2);

  # Or one can pass the factory an alignment and one or more
  # unaligned sequences to be added to the alignment. For example:

  # $seq is a Bio::Seq object.
  $aln = $factory->profile_align($aln1,$seq);

  #There are various additional options and input formats available.
  #See the DESCRIPTION section that follows for additional details.

=head1 DESCRIPTION

Note: this DESCRIPTION only documents the (Bio)perl interface to
TCoffee.

=head2 Helping the module find your executable

You will need to enable TCoffee to find the t_coffee program. This
can be done in (at least) three ways:

 1. Make sure the t_coffee executable is in your path so that
    which t_coffee returns a t_coffee executable on your system.

 2. Define an environmental variable TCOFFEEDIR which is a dir
    which contains the 't_coffee' app:
    In bash
    export TCOFFEEDIR=/home/username/progs/T-COFFEE_distribution_Version_1.37/bin
    In csh/tcsh
    setenv TCOFFEEDIR /home/username/progs/T-COFFEE_distribution_Version_1.37/bin

 3. Include a definition of an environmental variable TCOFFEEDIR in
    every script that will use this TCoffee wrapper module.
    BEGIN { $ENV{TCOFFEDIR} = '/home/username/progs/T-COFFEE_distribution_Version_1.37/bin' }
    use Bio::Tools::Run::Alignment::TCoffee;

If you are running an application on a webserver make sure the
webserver environment has the proper PATH set or use the options 2 or
3 to set the variables.

=head1 INTERNAL METHODS

=head2 _numeric_version

Version "numbers" are not numeric values.  In the case of T-Coffee,
they have an hash component at their end.  This was not the case in
older releases.  We use the first two numeric parts to do different
things though.  See also issue #1.

=head2 _run

 Title   :  _run
 Usage   :  Internal function, not to be called directly
 Function:  makes actual system call to tcoffee program
 Example :
 Returns : nothing; tcoffee output is written to a
           temporary file OR specified output file
 Args    : Name of a file containing a set of unaligned fasta sequences
           and hash of parameters to be passed to tcoffee

=head2 _setinput

 Title   :  _setinput
 Usage   :  Internal function, not to be called directly
 Function:  Create input file for tcoffee program
 Example :
 Returns : name of file containing tcoffee data input AND
           type of file (if known, S for sequence, L for sequence library,
           A for sequence alignment)
 Args    : Seq or Align object reference or input file name

=head2 _setparams

 Title   :  _setparams
 Usage   :  Internal function, not to be called directly
 Function:  Create parameter inputs for tcoffee program
 Example :
 Returns : parameter string to be passed to tcoffee
           during align or profile_align
 Args    : name of calling object

=head1 PARAMETERS FOR ALIGNMENT COMPUTATION

There are a number of possible parameters one can pass in TCoffee.
One should really read the online manual for the best explanation of
all the features.  See
http://igs-server.cnrs-mrs.fr/~cnotred/Documentation/t_coffee/t_coffee_doc.html

These can be specified as parameters when instantiating a new TCoffee
object, or through get/set methods of the same name (lowercase).