| Bio::Tools::Run::Alignment::DBA(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Alignment::DBA(3pm) |
Bio::Tools::Run::Alignment::DBA - Object for the alignment of two sequences using the DNA Block Aligner program.
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);
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.
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
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.
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/
Email shawnh@fugu-sg.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args :
Title : version Usage : exit if $prog->version() < 1.8 Function: Determine the version number of the program Example : Returns : float or undef Args : none
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.
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
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
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
Title : _query_seq Usage : Internal function, not to be called directly Function: get/set for the query sequence Example : Returns : Args :
Title : _subject_seq Usage : Internal function, not to be called directly Function: get/set for the subject sequence Example : Returns : Args :
| 2018-09-14 | perl v5.26.2 |