Bio::Tools::Run::Alignment::Probcons - Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Probcons program # Build a muscle alignment factory $factory = new Bio::Tools::Run::Alignment::Probcons (@params); # Pass the factory a list of sequences to be aligned. $inputfilename = 't/cysprot.fa'; # $aln is a SimpleAlign object. $aln = $factory->align($inputfilename); # or where @seq_array is an array of Bio::Seq objects $seq_array_ref = \@seq_array; $aln = $factory->align($seq_array_ref); # Or one can pass the factory a pair of (sub)alignments #to be aligned against each other, e.g.: #There are various additional options and input formats available. #See the DESCRIPTION section that follows for additional details. #To run probcons with training, try something like: #First round to generate train.params $factory = new Bio::Tools::Run::Alignment::Probcons ( 'iterative-refinement' => '1000', 'consistency' => '5', 'pre-training' => '20', 'emissions' => '', 'verbose' => '', 'train' => "$dir/$subdir/$outdir/train.params", ); $factory->outfile_name("$dir/$subdir/$outdir/train.params"); #Second round to use train.params to get a high qual alignment $seq_array_ref = \@seq_array; $aln = $factory->align($seq_array_ref); $aln = ''; $factory = ''; $factory = new Bio::Tools::Run::Alignment::Probcons ( 'iterative-refinement' => '1000', 'consistency' => '5', 'pre-training' => '20', 'verbose' => '', 'paramfile' => "$dir/$subdir/$outdir/train.params", ); $factory->outfile_name("$dir/$subdir/$outdir/outfile.afa"); $aln = $factory->align($seq_array_ref); Probcons is a Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences. You can get it and see information about it at this URL http://probcons.stanford.edu/

Helping the module find your executable
You will need to enable Probcons to find the probcons program. This can be done in (at least) three ways: 1. Make sure the probcons executable is in your path (i.e. 'which probcons' returns a valid program 2. define an environmental variable PROBCONSDIR which points to a directory containing the 'probcons' app: In bash export PROBCONSDIR=/home/progs/probcons or In csh/tcsh setenv PROBCONSDIR /home/progs/probcons 3. include a definition of an environmental variable PROBCONSDIR in every script that will BEGIN {$ENV{PROBCONSDIR} = '/home/progs/probcons'; } use Bio::Tools::Run::Alignment::Probcons;

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.open-bio.org/ Email jason-at-bioperl-dot-org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

program_name
Title : program_name Usage : $factory->program_name() Function: holds the program name Returns: string Args : None

program_dir
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtiained from ENV variable. Returns: string Args :

new
Title : new Usage : my $probcons = Bio::Tools::Run::Alignment::Probcons->new(); Function: Constructor Returns : Bio::Tools::Run::Alignment::Probcons Args : -outfile_name => $outname

error_string
Title : error_string Usage : $obj->error_string($newval) Function: Where the output from the last analysus run is stored. Returns : value of error_string Args : newvalue (optional)

version
Title : version Usage : exit if $prog->version() < 1.8 Function: Determine the version number of the program Example : Returns : float or undef Args : none

run
Title : run Usage : my $output = $application->run(\@seqs); Function: Generic run of an application Returns : Bio::SimpleAlign object Args : Arrayref of Bio::PrimarySeqI objects or a filename to run on

align
Title : align Usage : $inputfilename = 't/data/cysprot.fa'; $aln = $factory->align($inputfilename); or $seq_array_ref = \@seq_array; # @seq_array is array of Seq objs $aln = $factory->align($seq_array_ref); Function: Perform a multiple sequence alignment Returns : Reference to a SimpleAlign object containing the sequence alignment. Args : Name of a file containing a set of unaligned fasta sequences or else an array of references to Bio::Seq objects. Throws an exception if argument is not either a string (eg a filename) or a reference to an array of Bio::Seq objects. If argument is string, throws exception if file corresponding to string name can not be found. If argument is Bio::Seq array, throws exception if less than two sequence objects are in array.

_run
Title : _run Usage : Internal function, not to be called directly Function: makes actual system call to probcons program Example : Returns : nothing; probcons output is written to a temporary file OR specified output file Args : Name of a file containing a set of unaligned fasta sequences and hash of parameters to be passed to probcons

_setinput
Title : _setinput Usage : Internal function, not to be called directly Function: Create input file for probcons program Example : Returns : name of file containing probcons data input AND Args : Arrayref of Seqs or input file name

_setparams
Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for probcons program Example : Returns : parameter string to be passed to probcons during align or profile_align Args : name of calling object

aformat
Title : aformat Usage : my $alignmentformat = $self->aformat(); Function: Get/Set alignment format Returns : string Args : string

no_param_checks
Title : no_param_checks Usage : $obj->no_param_checks($newval) Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values Returns : value of no_param_checks Args : newvalue (optional)

save_tempfiles
Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional)

outfile_name
Title : outfile_name Usage : my $outfile = $probcons->outfile_name(); Function: Get/Set the name of the output file for this run (if you wanted to do something special) Returns : string Args : [optional] string to set value to

tempdir
Title : tempdir Usage : my $tmpdir = $self->tempdir(); Function: Retrieve a temporary directory name (which is created) Returns : string which is the name of the temporary directory Args : none

cleanup
Title : cleanup Usage : $probcons->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none

io
Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<Bio::Root::IO> Args : none