dba

Bio::Tools::Run::Alignment::DBA(3pm)			User Contributed Perl Documentation		      Bio::Tools::Run::Alignment::DBA(3pm)

NAME

       Bio::Tools::Run::Alignment::DBA - Object for the alignment of two sequences using the DNA Block Aligner program.

SYNOPSIS

	 use Bio::Tools::Run::Alignment::DBA;

	 #  Build a dba alignment factory
	 my @params = ('matchA' => 0.75,
			'matchB' => '0.55',
			'dymem' =>'linear');
	 my $factory = Bio::Tools::Run::Alignment::DBA->new(@params);

	 #  Pass the factory a filename with 2 sequences to be aligned.
	 $inputfilename = 't/data/dbaseq.fa';
	 # @hsps is an array of GenericHSP objects
	 my @hsps = $factory->align($inputfilename);

	 # or
	 my @files = ('t/data/dbaseq1.fa','t/data/dbaseq2.fa');
	 my @hsps = $factory->align(@files);

	 # or where @seq_array is an array of Bio::Seq objects
	 $seq_array_ref = @seq_array;
	 my @hsps = $factory->align($seq_array_ref);

DESCRIPTION

       DNA Block Aligner program (DBA) was developed by Ewan Birney. DBA is part of the Wise package available at
       <http://www.sanger.ac.uk/software/wise2>.

       You will need to enable dba to find the dba program. This can be done in a few different ways:

       1. Define an environmental variable WISEDIR:

	 export WISEDIR =/usr/local/share/wise2.2.0

       2. Include a definition of an environmental variable WISEDIR in every script that will use DBA.pm:

	 $ENV{WISEDIR} = '/usr/local/share/wise2.2.20';

       3. Make sure that the dba application is in your PATH.

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

   Support
       Please direct usage questions or support issues to the mailing list:

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

AUTHOR - Shawn Hoon
       Email shawnh@fugu-sg.org

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, obtained from ENV variable.
	Returns:  string
	Args	:

   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

   align
	Title	: align
	Usage	:
		   $inputfilename = 't/data/seq.fa';
		   @hsps = $factory->align($inputfilename);
		 or
		   #@seq_array is array of Seq objs
		   $seq_array_ref = @seq_array;
		   @hsps = $factory->align($seq_array_ref);
		 or
		   my @files = ('t/data/seq1.fa','t/data/seq2.fa');
		   @hsps = $factory->align(@files);
	Function: Perform a DBA  alignment

	Returns : An array of Bio::Search::HSP::GenericHSP objects
	Args	: Name of a file containing a set of 2 fasta sequences
		  or else a reference to an array  to 2  Bio::Seq objects.
		  or else a reference to an array of 2 file
		     names containing 1 fasta sequence each

	Throws an exception if argument is not either a string (eg a
	filename) or a reference to an array of 2 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 dba program
	Example :
	Returns : nothing; dba	output is written to a temp file
	Args	: Name of a file containing a set of unaligned fasta sequences
		  and hash of parameters to be passed to dba

   _parse_results
	Title	:  __parse_results
	Usage	:  Internal function, not to be called directly
	Function:  Parses dba output
	Example :
	Returns : an reference to an array of GenericHSPs
	Args	: the name of the output file

   _setinput()
	Title	:  _setinput
	Usage	:  Internal function, not to be called directly
	Function:   Create input file for dba program
	Example :
	Returns : name of file containing dba data input
	Args	: Seq or Align object reference or input file name

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

   _query_seq()
	Title	:  _query_seq
	Usage	:  Internal function, not to be called directly
	Function:  get/set for the query sequence
	Example :
	Returns :
	Args	:

   _subject_seq()
	Title	:  _subject_seq
	Usage	:  Internal function, not to be called directly
	Function:  get/set for the subject sequence
	Example :
	Returns :

	Args	:

perl v5.12.3							    2011-06-18				      Bio::Tools::Run::Alignment::DBA(3pm)