Bio::Tools::Run::Alignment::Lagan - Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)
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, );
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.
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.
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Please direct usage questions or support issues to the mailing list:
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.
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:
Genome Sciences Centre in beautiful Vancouver, British Columbia CANADA
MLagan/Lagan is the hard work of Michael Brudno et al.
Sendu Bala email@example.com
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
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.
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.
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
Title : _generic_lagan Usage : internal function not called directly Returns : SimpleAlign object
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
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
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
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
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
Title : version Usage : my $version = $lagan->version; Function: returns the program version Returns : number Args : none