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DBA Companion 1.6 (Default branch)
12-24-2008
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Bio::Tools::Run::Alignment::DBA(3pm) User Contributed Perl Documentation Bio::Tools::Run::Alignment::DBA(3pm) 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 : perl v5.12.3 2011-06-18 Bio::Tools::Run::Alignment::DBA(3pm)