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
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 :