Bio::Tools::Run::Alignment::Lagan(3)

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, the executables "mlagan" and "lagan.pl" must be in your path or you must have an environment variable that points to the executable directory "LAGANDIR=/opt/lagan_executables/"

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

A SimpleAlign object is returned.

TO USE MLAGAN:

  my $lagan = new Bio::Tools::Run::Alignment::Lagan();
  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/MailList.shtml  - About the mailing lists

  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 email or the web:

  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.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.

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
  Returns an SimpleAlign object / preloaded with the tmp file of the Mlagan multifasta output.

  _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