Bio::T...Pal2Nal(3pm)

NAME 💅

Bio::Tools::Run::Alignment::Pal2Nal — ok bestie, it's a wrapper for Pal2Nal 🎀

(yes, this is the page for Bio::T...Pal2Nal(3pm), from the User Contributed Perl Documentation set, and we're about to make it make sense 💖)

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SYNOPSIS ✨

use Bio::Tools::Run::Alignment::Pal2Nal;

# Make a Pal2Nal factory
$factory = Bio::Tools::Run::Alignment::Pal2Nal->new();

# Run Pal2Nal with a protein alignment file and a multi-fasta nucleotide
# file
my $aln = $factory->run($protein_alignfilename, $nucleotide_filename);

# or with Bioperl objects
$aln = $factory->run($protein_bio_simplalign, [$nucleotide_bio_seq1,
                                               $nucleotide_bio_seq2]);

# combinations of files/ objects are possible

# $aln isa Bio::SimpleAlign of the nucleotide sequences aligned according to
# the protein alignment

Like, that's the whole vibe right there 🦋

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DESCRIPTION 🌸

So this is a wrapper for running the Pal2Nal perl script by Mikita Suyama. You can get details here: http://coot.embl.de/pal2nal/. Pal2Nal is used for aligning a set of nucleotide sequences based on an alignment of their translations — that's the whole point of it, no cap 🧬

You can try supplying normal pal2nal command-line arguments to new(), eg. new(), or calling arg-named methods (excluding the initial hyphen, eg. $factory->(1) to set the - arg).

🫶 Heads up: you will need to enable this Pal2Nal wrapper to find the pal2nal.pl script. There are (at least) three ways to do that:

1. Make sure the script is in your path. 🚶♀️
2. Define an environmental variable PAL2NALDIR which is a directory which contains the script:

In bash:

export PAL2NALDIR=/home/username/pal2nal/

In csh/tcsh:

setenv PAL2NALDIR /home/username/pal2nal

3. Include a definition of an environmental variable PAL2NALDIR in every script that will use this Pal2Nal wrapper module, e.g.:

BEGIN { $ENV{PAL2NALDIR} = '/home/username/pal2nal/' }
use Bio::Tools::Run::Alignment::Pal2Nal;

Pick your fighter, bestie 💅

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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 the Bioperl mailing list. Your participation is much appreciated, fr fr 🙏

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 responsive 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 receipts you bring, the faster it gets fixed ✨

Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system to help us keep track of 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 - Sendu Bala 👑

Email bix@sendu.me.uk

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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: None

new 🦋

• Title: new
• Usage: $factory = Bio::Tools::Run::Alignment::Pal2Nal->new()
• Function: creates a new Pal2Nal factory.
• Returns: Bio::Tools::Run::Alignment::Pal2Nal
• Args: Most options understood by pal2nal.pl can be supplied as key => value pairs.

These options can NOT be used with this wrapper:

• -output
• -html
• -h
• -nostderr

run 🔥

• Title: run
• Usage:

$result = $factory->run($protein_align_file, $multi_fasta_nucleotide);
-or-
$result = $factory->run($prot_align_object, [$bioseq_object1, ...]);

• Function: Runs pal2nal on a protein alignment and set of nucleotide sequences.
• Returns: Bio::SimpleAlign;
• Args: The first argument represents a protein alignment, the second argument a set of nucleotide sequences.

The alignment can be provided as an alignment file readable by Bio::AlignIO, or a Bio::Align::AlignI compliant object (eg. a Bio::SimpleAlign).

The nucleotide sequences can be provided as a single filename of a fasta file containing multiple nucleotide sequences, or an array ref of filenames, each file containing one sequence. Alternatively, an array ref of Bio::PrimarySeqI compliant objects can be supplied.

💀 In all cases, the protein alignment sequence names must correspond to the names of the supplied nucleotide sequences. Like, they have to match. No matching = it's giving chaos.

_setparams 🙈

• Title: _setparams
• Usage: Internal function, not to be called directly
• Function: Creates a string of params to be used in the command string
• Returns: string of params
• Args: alignment and tree file names

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And that's the whole page, bestie — you ate it, periodt 👑 This was Bio::T...Pal2Nal(3pm) from perl v5.36.0, dated 2023-01-22 💖 ✨ 🌈 🫶