Bio::Tools::Run::Alignment::DBA.3pm

Langue: en

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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://bugzilla.open-bio.org/
 
 

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    :