Bio::Tools::Run::Alignment::Lagan man page on Pidora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Pidora logo
[printable version]

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://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

perl v5.14.1			  2011-07-Bio::Tools::Run::Alignment::Lagan(3)
[top]

List of man pages available for Pidora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net