Helping the module find your executable

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

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

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://redmine.open-bio.org/projects/bioperl/

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    :

new

 Title   : new
 Usage   : my $kalign = Bio::Tools::Run::Alignment::Kalign->new();
 Function: Constructor
 Returns : Bio::Tools::Run::Alignment::Kalign
 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() < 2
 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 kalign program
 Example :
 Returns : nothing; kalign 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 kalign

_setinput

 Title   :  _setinput
 Usage   :  Internal function, not to be called directly        
 Function:  Create input file for kalign program
 Example :
 Returns : name of file containing kalign 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 kalign program
 Example :
 Returns : parameter string to be passed to kalign
           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 = $kalign->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   : $kalign->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