/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Alignment::DBA

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    :