Bio::T...nt::DBA(3pm)

💖 NAME 💖

okay bestie, gather round, because this is the Bio::T...nt::DBA(3pm) page and it's giving biotech excellence 🧬✨

Bio::Tools::Run::Alignment::DBA — it's an object for aligning two sequences using the DNA Block Aligner program. two sequences. that's it. that's the whole job. and it slays at it 💅

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🌸 SYNOPSIS 🌸

like, here's the vibe, no cap:

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);

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✨ DESCRIPTION ✨

so the DNA Block Aligner program (DBA) was developed by Ewan Birney — iconic behaviour, honestly 👑 — and DBA is part of the Wise package, which lives at http://www.sanger.ac.uk/software/wise2 if you wanna go look.

now listen, you will need to enable dba to find the dba program. there's a few different ways to do this, pick your fighter:

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.

three options, all valid, all valid, we love choices 🎀

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🫶 FEEDBACK 🫶

📬 Mailing Lists 📬

user feedback is an integral part of the evolution of this and other Bioperl modules — like fr, your voice matters here 💜 send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated, genuinely 🥹

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. because like, 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 — the more context the better, bestie, it's giving considerate 🌸

🐛 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/

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👑 AUTHOR - Shawn Hoon 👑

Email shawnh@fugu-sg.org — main character energy, thank you for your service 🫡💖

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🔮 APPENDIX 🔮

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — iykyk, don't touch those unless you know what you're doing 🙈

🧚 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

ok this is the important bit so listen up 🚨 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. it will literally yell at you and honestly? fair 💀

🧚 _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:

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and that's the whole page, bestie 🫶 this beauty ships as perl v5.36.0, dated 2023-01-22, and yes the footer is still out here calling it Bio::T...nt::DBA(3pm) because some things never change 💅✨