Helping the module find your executable

  1. Make sure the msaprobs executable is in your path (i.e. 
     'which msaprobs' returns a valid program)
  2. define an environmental variable MSAPROBSDIR which points to a 
     directory containing the 'msaprobs' app:
   In bash 
        export MSAPROBSDIR=/home/progs/msaprobs   or
   In csh/tcsh
        setenv MSAPROBSDIR /home/progs/msaprobs

  3. include a definition of an environmental variable MSAPROBSDIR 
      in every script that will
     BEGIN {$ENV{MSAPROBSDIR} = '/home/progs/msaprobs'; }
     use Bio::Tools::Run::Alignment::MSAProbs;

Mailing Lists

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

 http://bugzilla.open-bio.org/

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, obtained from ENV variable.
 Returns:  string
 Args    :

version

 Title   : version
 Usage   : exit if $prog->version() < 0.9.4
 Function: Determine the version number of the program
 Example :
 Returns : float or undef
 Args    : none

new

 Title   : new
 Usage   : my $msaprobs = Bio::Tools::Run::Alignment::MSAProbs->new();
 Function: Constructor
 Returns : Bio::Tools::Run::Alignment::MSAProbs
 Args    : -outfile => $outname

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.

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)

infile

 Title   : infile
 Usage   : $prog->infile($filename)
 Function: get/set the fasta (and only a fasta) file to run on
           or the array reference containing the Bio::SeqI objects
 Returns : name of input sequence file or object array ref
 Args    : name of input sequence file or object array ref

outfile

 Title   : outfile
 Usage   : $prog->outfile($filename)
 Function: get/set the file to save output to
 Returns : outfile name if set
 Args    : newvalue (optional)

annot_file

 Title   : annot_file
 Usage   : $prog->annot_file($filename)
 Function: get/set the file name to write the MSA annotation to
 Returns : filename or undef
 Args    : filename (optional)

num_threads

 Title   : num_threads
 Usage   : $prog->num_threads($cores)
 Function: get/set number of cores on your machine
 Returns : integer
 Args    : integer (optional; executable auto-detects)

consistency

 Title   : consistency
 Usage   : $prog->consistency($passes)
 Function: get/set the number of consistency transformation passes
 Returns : integer
 Args    : integer 0..5, [default 2] (optional)

iterations

 Title   : iterations
 Usage   : $prog->iterations($passes)
 Function: get/set the number of iterative-refinement passes
 Returns : integer
 Args    : integer 0..1000, [default 10] (optional)

alignment_order

 Title   : alignment_order
 Usage   : $prog->alignment_order($bool)
 Function: specify whether or not to output aligned sequences in
           alignment order, not input order
 Returns : boolean
 Args    : boolean [default: off] (optional)

clustalw

 Title   : clustalw
 Usage   : $prog->clustalw($bool)
 Function: write output in clustalw format; makes no sense unless
           outfile() is also specified
 Returns : boolean
 Args    : boolean [default: off] (optional)

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 = $msaprobs->outfile_name();
 Function: Get the name of the output file from a run
           (if you wanted to do something special)
 Returns : string
 Args    : none

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   : $msaprobs->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

_run

 Title   :  _run
 Usage   :  Internal function, not to be called directly        
 Function:  makes actual system call to msaprobs program
 Example :
 Returns : nothing; msaprobs 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 msaprobs

_setinput

 Title   :  _setinput
 Usage   :  Internal function, not to be called directly        
 Function:  Create input file for msaprobs program
 Example :
 Returns : name of file containing msaprobs 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 msaprobs program
 Example :
 Returns : parameter string to be passed to msaprobs
           during align
 Args    : name of calling object

aformat

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