/ 
bioperl-run-1.5.2_100
/ Bio::Tools::Run::Alignment::Kalign

NAME

Bio::Tools::Run::Alignment::Kalign - Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the KALIGN program

SYNOPSIS

# Build a kalign alignment factory
$factory = new Bio::Tools::Run::Alignment::Kalign (@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.

DESCRIPTION

Please cite:

Timo Lassmann and Erik L.L. Sonnhammer (2005)
Kalign - an accurate and fast multiple sequence alignment algorithm.
BMC Bioinformatics 6:298

http://msa.cgb.ki.se/downloads/kalign/current.tar.gz

Helping the module find your executable

You will need to enable Kalign to find the kalign program. This can be done in (at least) three ways:

  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;

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 one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - 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/

AUTHOR - Albert Vilella

Email idontlikespam@hotmail.com

APPENDIX

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 $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

Bio::Tools::Run::BaseWrapper methods

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