Bio::T...Kalign(3pm)

💖 Bio::Tools::Run::Alignment::Kalign 💖

okay bestie, gather round, because this is the 3pm manual page for Bio::Tools::Run::Alignment::Kalign — the Perl module that lets you build an object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the KALIGN program. yes. all of that. it's giving science and it's giving slay. 🧬✨

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✨ NAME ✨

Bio::Tools::Run::Alignment::Kalign — Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the KALIGN program.

🎀 SYNOPSIS 🎀

  # Build a kalign alignment factory
  $factory = Bio::Tools::Run::Alignment::Kalign->new(@params);

  # Pass the factory a list of sequences to be aligned.
  $inputfilename = 't/cysprot.fa';
  # $aln is a SimpleAlign object.
  $aln = $factory->align($inputfilename);

  # or where @seq_array is an array of Bio::Seq objects
  $seq_array_ref = \@seq_array;
  $aln = $factory->align($seq_array_ref);

  # Or one can pass the factory a pair of (sub)alignments
  #to be aligned against each other, e.g.:

  #There are various additional options and input formats available.
  #See the DESCRIPTION section that follows for additional details.

🌸 DESCRIPTION 🌸

Please cite:

        Timo Lassmann and Erik L.L. Sonnhammer (2005)
        Kalign - an accurate and fast multiple sequence alignment algorithm.
        BMC Bioinformatics 6:298

http://msa.cgb.ki.se/downloads/kalign/current.tar.gz

🦋 Helping the module find your executable 🦋

You will need to enable Kalign to find the kalign program. This can be done in (at least) three ways:

1. Make sure the kalign executable is in your path (i.e. which kalign returns a valid program
2. define an environmental variable KALIGNDIR which points to a directory containing the kalign app:

In bash

export KALIGNDIR=/home/progs/kalign   or

In csh/tcsh

setenv KALIGNDIR /home/progs/kalign

3. include a definition of an environmental variable KALIGNDIR in every script that will

BEGIN {$ENV{KALIGNDIR} = '/home/progs/kalign'; }
use Bio::Tools::Run::Alignment::Kalign;

fr fr bestie, pick one of these, you don't need all three. the module just needs to know where kalign lives. 🫶

💌 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. no cap, they actually read these.

  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/

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👑 AUTHOR - Albert Vilella 👑

Email idontlikespam@hotmail.com

🌈 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:

⭐ new ⭐

• Title: new
• Usage: my $kalign = Bio::Tools::Run::Alignment::Kalign->new();
• Function: Constructor
• Returns: Bio::Tools::Run::Alignment::Kalign
• Args: -outfile_name => $outname

⭐ error_string ⭐

• Title: error_string
• Usage: $obj->error_string($newval)
• Function: Where the output from the last analysus run is stored.
• Returns: value of error_string
• Args: newvalue (optional)

⭐ version ⭐

• Title: version
• Usage: exit if $prog->version() < 2
• Function: Determine the version number of the program
• Example:
• Returns: float or undef
• Args: none

⭐ run ⭐

• Title: run
• Usage: my $output = $application->run(\@seqs);
• Function: Generic run of an application
• Returns: Bio::SimpleAlign object
• Args: Arrayref of Bio::PrimarySeqI objects or a filename to run on

⭐ align ⭐

• Title: align
• Usage:

        $inputfilename = 't/data/cysprot.fa';
        $aln = $factory->align($inputfilename);
    or
        $seq_array_ref = \@seq_array;
        # @seq_array is array of Seq objs
        $aln = $factory->align($seq_array_ref);

• Function: Perform a multiple sequence alignment
• Returns: Reference to a SimpleAlign object containing the sequence alignment.
• Args: Name of a file containing a set of unaligned fasta sequences or else an array of references to Bio::Seq objects.

Throws an exception if argument is not either a string (eg a filename) or a reference to an array of 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.

💀 yes bestie, it will throw. less than two sequences? exception. bad filename? exception. the vibe check is strict and honestly? iconic.

⭐ _run ⭐

• Title: _run
• Usage: Internal function, not to be called directly
• Function: makes actual system call to kalign program
• Example:
• Returns: nothing; kalign output is written to a temporary file OR specified output file
• Args: Name of a file containing a set of unaligned fasta sequences and hash of parameters to be passed to kalign

⭐ _setinput ⭐

• Title: _setinput
• Usage: Internal function, not to be called directly
• Function: Create input file for kalign program
• Example:
• Returns: name of file containing kalign data input AND
• Args: Arrayref of Seqs or input file name

⭐ _setparams ⭐

• Title: _setparams
• Usage: Internal function, not to be called directly
• Function: Create parameter inputs for kalign program
• Example:
• Returns: parameter string to be passed to kalign during align or profile_align
• Args: name of calling object

⭐ aformat ⭐

• Title: aformat
• Usage: my $alignmentformat = $self->aformat();
• Function: Get/Set alignment format
• Returns: string
• Args: string

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💅 Bio::Tools::Run::BaseWrapper methods 💅

🌟 no_param_checks 🌟

• Title: no_param_checks
• Usage: $obj->no_param_checks($newval)
• Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values
• Returns: value of no_param_checks
• Args: newvalue (optional)

🌟 save_tempfiles 🌟

• Title: save_tempfiles
• Usage: $obj->save_tempfiles($newval)
• Function:
• Returns: value of save_tempfiles
• Args: newvalue (optional)

🌟 outfile_name 🌟

• Title: outfile_name
• Usage: my $outfile = $kalign->outfile_name();
• Function: Get/Set the name of the output file for this run (if you wanted to do something special)
• Returns: string
• Args: [optional] string to set value to

🌟 tempdir 🌟

• Title: tempdir
• Usage: my $tmpdir = $self->tempdir();
• Function: Retrieve a temporary directory name (which is created)
• Returns: string which is the name of the temporary directory
• Args: none

🌟 cleanup 🌟

• Title: cleanup
• Usage: $kalign->cleanup();
• Function: Will cleanup the tempdir directory
• Returns: none
• Args: none

🌟 io 🌟

• Title: io
• Usage: $obj->io($newval)
• Function: Gets a Bio::Root::IO object
• Returns: Bio::Root::IO
• Args: none

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and that's the whole page, bestie 🎀 this was perl v5.36.0, dated 2023-01-22, filed under Bio::T...Kalign(3pm) — go align something gorgeous 💖✨