Christopher Fields > BioPerl-Run > Bio::Tools::Run::Alignment::DBA

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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    :
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