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Bio::Tools::Run::AlignUser:Contributed PerBio::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, 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://redmine.open-bio.org/projects/bioperl/

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

perl v5.32.1			  2021-03-Bio::Tools::Run::Alignment::Lagan(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Stephen Montgomery | CONTRIBUTORS | APPENDIX

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