Bio::Tools::Run::Alignment::Lagan.3pm

Langue: en

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::Alignment::Lagan - Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)

SYNOPSIS

   use Bio::Tools::Run::Alignment::Lagan;
 
   @params =
       ('chaos' => "The contents of this string will be passed as args to chaos",
 
        #Read you chaos README file for more info/This functionality
        #has not been tested and will be integrated in future versions.
 
        'order' => "\"-gs -7 -gc -2 -mt 2 -ms -1\"",
        #Where gap start penalty of- 7, gap continue of -2, match of 2,
        #and mismatch of -1.
 
        'recurse' => "\"(12,25),(7,25),(4,30)"\",
        #A list of (wordlength,score cutoff) pairs to be used in the
        #recursive anchoring
 
        'tree' => "\"(sample1 (sample2 sample3))"\",
        #Used by mlagan / tree can also be passed when calling mlagan directly
 
        #SCORING PARAMETERS FOR MLAGAN:
        'match' => 12,
        'mismatch' => -8,
        'gapstart' => -50,
        'gapend' => -50,
        'gapcont' => -2,
   );
 
 

DESCRIPTION

To run mlagan/lagan, you must have an environment variable that points to the executable directory with files lagan.pl etc. ``LAGAN_DIR=/opt/lagan_executables/''

Simply having the executables in your path is not supported because the executables themselves only work with the environment variable set.

All lagan and mlagan parameters listed in their Readmes can be set except for the mfa flag which has been turned on by default to prevent parsing of the alignment format.

TO USE LAGAN:

   my $lagan = Bio::Tools::Run::Alignment::Lagan->new(@params);
   my $report_out = $lagan->lagan($seq1, $seq2);
 
 

A SimpleAlign object is returned.

TO USE MLAGAN:

   my $lagan = Bio::Tools::Run::Alignment::Lagan->new();
   my $tree = "(($seqname1 $seqname2) $seqname3)";
   my @sequence_objs;    #an array of bioperl Seq objects
 
   ##If you use an unblessed seq array
   my $seq_ref = \@sequence_objs;
   bless $seq_ref, "ARRAY";
 
   my $report_out = $lagan->mlagan($seq_ref, $tree);
 
   A SimpleAlign object is returned
 
 

Only basic mlagan/lagan functionality has been implemented due to the iterative development of their project. Future maintenance upgrades will include enhanced features and scoring.

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://bugzilla.open-bio.org/
 
 

AUTHOR - Stephen Montgomery

Email smontgom@bcgsc.bc.ca

Genome Sciences Centre in beautiful Vancouver, British Columbia CANADA

CONTRIBUTORS

MLagan/Lagan is the hard work of Michael Brudno et al.

Sendu Bala bix@sendu.me.uk

APPENDIX

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

lagan

   Runs the Lagan pairwise alignment algorithm
   Inputs should be two PrimarySeq objects.
 
   Returns an SimpleAlign object / preloaded with the tmp file of the
   Lagan multifasta output.
 
 

mlagan

   Runs the Mlagan multiple sequence alignment algorithm.
   Inputs should be an Array of Primary Seq objects and a Phylogenetic Tree in
   String format or as a Bio::Tree::TreeI compliant object.
   Returns an SimpleAlign object / preloaded with the tmp file of the Mlagan
   multifasta output.
 
 

nuc_matrix

  Title   : nuc_matrix
  Usage   : my $matrix_obj = $obj->nuc_matrix();
            -or-
            $obj->nuc_matrix($matrix_obj);
            -or-
            $obj->nuc_matrix($matrix_file);
  Function: Get/set the substitution matrix for use by mlagan. By default the
            file $LAGAN_DIR/nucmatrix.txt is used by mlagan. By default this
            method returns a corresponding Matrix.
  Returns : Bio::Matrix::Mlagan object
  Args    : none to get, OR to set:
            Bio::Matrix::MLagan object
            OR
            filename of an mlagan substitution matrix file
 
            NB: due to a bug in mlagan 2.0, the -nucmatrixfile option does not
            work, so this Bioperl wrapper is unable to simply point mlagan to
            your desired matrix file (or to a temp file generated from your
            matrix object). Instead the $LAGAN_DIR/nucmatrix.txt file must
            actually be replaced. This wrapper will make a back-up copy of that
            file, write the new file in its place, then revert things back to the
            way they were after the alignment has been produced. For this reason,
            $LAGAN_DIR must be writable, as must $LAGAN_DIR/nucmatrix.txt.
 
 

_setinput

  Title   : _setinput
  Usage   : Internal function, not to be called directly
  Function: Create input file(s) for Lagan executables
  Returns : name of files containing Lagan data input / 
            or array of files and phylo tree for Mlagan data input
 
 

_generic_lagan

  Title   : _generic_lagan
  Usage   :  internal function not called directly
  Returns :  SimpleAlign object
 
 

_setparams

  Title   : _setparams
  Usage   : Internal function, not to be called directly
  Function: Create parameter inputs for (m)Lagan program
  Returns : parameter string to be passed to Lagan
  Args    : Reference to calling object and name of (m)Lagan executable
 
 

_runlagan

  Title   :  _runlagan
  Usage   :  Internal function, not to be called directly
  Function:   makes actual system call to (m)Lagan program
  Example :
  Returns : Report object in the SimpleAlign object
 
 

executable

  Title   : executable
  Usage   : my $exe = $lagan->executable('mlagan');
  Function: Finds the full path to the 'lagan' 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
 
  Thanks to Jason Stajich for providing the framework for this subroutine
 
 

program_path

  Title   : program_path
  Usage   : my $path = $lagan->program_path();
  Function: Builds path for executable
  Returns : string representing the full path to the exe
 
  Thanks to Jason Stajich for providing the framework for this subroutine
 
 

program_dir

  Title   : program_dir
  Usage   : my $dir = $lagan->program_dir();
  Function: Abstract get method for dir of program. To be implemented
            by wrapper.
  Returns : string representing program directory
 
  Thanks to Jason Stajich for providing the framework for this subroutine
 
 

version

  Title   : version
  Usage   : my $version = $lagan->version;
  Function: returns the program version
  Returns : number
  Args    : none