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

💖 Bio::T...::MAFFT — the perl manual page, but make it cute

okay so bestie, welcome to Bio::Tools::Run::Alignment::MAFFT(3pm) from the User Contributed Perl Documentation ✨ this is the page that tells you how to run the MAFFT alignment tools from Perl, and honestly? she's iconic. let's get into it 💅

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🌸 NAME 🌸

Bio::Tools::Run::Alignment::MAFFT — run the MAFFT alignment tools 🧚

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✨ SYNOPSIS ✨

no cap, this is the whole vibe in four little bites:

# Build a MAFFT alignment factory
$factory = Bio::Tools::Run::Alignment::MAFFT->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);

#There are various additional options available.

like, build the factory, hand it sequences, get an alignment back. main character energy fr fr 👑

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🦋 DESCRIPTION 🦋

you can get MAFFT from <http://mafft.cbrc.jp/alignment/software/> — go get her 🫶

"fftnsi" is the default method for Mafft version 4 in this implementation. that's the default, periodt.

want to know how to specify parameters to the underlying alignment program? go read Bio::Tools::Run::Alignment::Clustalw for that description. and for a description of the MAFFT parameters themselves, check the MAFFT manual page 📖

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💬 FEEDBACK 💬

📬 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules, literally. 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/MailList.html - 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. there are so many experienced and reponsive experts who 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 deets the better, bestie.

🐛 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 - Jason Stajich 👑

Email jason-at-bioperl.org 💌

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🎀 APPENDIX 🎀

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk, that underscore means don't touch unless you know what you're doing).

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program_name

Title   : program_name
Usage   : $factory->program_name()
Function: holds the program name
Returns:  string
Args    : None

she just holds the program name. simple, effective, slay.

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executable

Title   : executable
Usage   : my $exe = $blastfactory->executable('blastall');
Function: Finds the full path to the 'codeml' executable
Returns : string representing the full path to the exe
Args    : [optional] name of executable to set path to
          [optional] boolean flag whether or not warn when exe is not found

finds the full path to the 'codeml' executable 🌈 returns a string of the full path to the exe. you can optionally pass the name of an executable to set the path to, and optionally a boolean flag for whether or not to warn when the exe is not found 🔍

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program_path

Title   : program_path
Usage   : my $path = $factory->program_path();
Function: Builds path for executable
Returns : string representing the full path to the exe
Args    : none

builds the path for the executable and hands you back a string of that full path. no args, no drama 💅

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program_dir

Title   : program_dir
Usage   : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns:  string
Args    :

returns the program directory, which she gets from an ENV variable 🌱 returns a string.

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error_string

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

this is where the output from the last analysis run is stored 📝 returns the value of error_string, and you can optionally pass a newvalue.

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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

determines the version number of the program 🔢 returns a float or undef. no args, she just knows.

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run

Title   : run
Usage   : my $output = $application->run(\@seqs);
Function: Generic run of an application
Returns : Bio::SimpleAlign object
Args    : array ref of Bio::PrimarySeqI objects OR
          filename of sequences to run with

the generic run of an application 🏃♀️💨 returns a Bio::SimpleAlign object. args are either an array ref of Bio::PrimarySeqI objects or a filename of sequences to run with.

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align

Title   : align
Usage   :
   $inputfilename = 't/data/cysprot.fa';
   $aln = $factory->align($inputfilename);
or
   $seq_array_ref = \@seq_array;
   # @seq_array is an 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.

okay so THIS is the one you actually want — performs a multiple sequence alignment and returns a reference to a SimpleAlign object containing the sequence alignment ✨ args are the name of a file containing a set of unaligned fasta sequences, or else an array of references to Bio::Seq objects.

⚠️ bestie listen: she throws an exception if the argument is not either a string (eg a filename) or a reference to an array of Bio::Seq objects. if the argument is a string, she throws an exception if the file corresponding to that string name can not be found 😭 and if the argument is a Bio::Seq array, she throws an exception if less than two sequence objects are in the array. so don't come at her with one lonely sequence. she will not be doing that.

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_run

Title   :  _run
Usage   :  Internal function, not to be called directly
Function:  makes actual system call to tcoffee program
Example :
Returns : nothing; tcoffee 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 tcoffee

internal function, not to be called directly 🙈 she makes the actual system call to the tcoffee program. returns nothing; the tcoffee output is written to a temporary file OR a specified output file. args are the name of a file containing a set of unaligned fasta sequences and a hash of parameters to be passed to tcoffee.

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_setinput

Title   :  _setinput
Usage   :  Internal function, not to be called directly
Function:  Create input file for mafft programs
Example :
Returns : name of file containing mafft data input
Args    : Seq or Align object reference or input file name

internal function, not to be called directly 🚫 creates the input file for mafft programs. returns the name of the file containing mafft data input. args are a Seq or Align object reference or an input file name.

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_setparams

Title   :  _setparams
Usage   :  Internal function, not to be called directly
Function:  Create parameter inputs for mafft program
Example :
Returns : parameter string to be passed to mafft program
Args    : name of calling object

internal function, not to be called directly 🚫 creates the parameter inputs for the mafft program. returns the parameter string to be passed to the mafft program. args are the name of the calling object.

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methods

Title   : methods
Usage   : my @methods = $self->methods()
Function: Get/Set Alignment methods - NOT VALIDATED
Returns : array of strings
Args    : arrayref of strings

get/set alignment methods — NOT VALIDATED 💀 like, she will not be checking your work here. returns an array of strings. args are an arrayref of strings.

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_version6

Title   : _version6
Usage   : Internal function, not to be called directly
Function: Check if the version of MAFFT is 6
Example :
Returns : Boolean
Args    : None

internal function, not to be called directly 🚫 checks if the version of MAFFT is 6. returns a Boolean. no args.

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🌈 Bio::Tools::Run::BaseWrapper methods 🌈

these are the inherited base-wrapper girls, coming through 💅

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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)

a Boolean flag as to whether or not we should trust the sanity checks for parameter values 🧠 returns the value of no_param_checks. optionally pass a newvalue.

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save_tempfiles

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

returns the value of save_tempfiles. optionally pass a newvalue. (the original leaves the Function line blank, and honestly? she said "figure it out" 💀)

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outfile_name

Title   : outfile_name
Usage   : my $outfile = $mafft->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

get/set the name of the output file for this run — you know, if you wanted to do something special ✨ returns a string. optionally pass a string to set the value to.

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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

retrieves a temporary directory name — and yes, she creates it too, it's not just a name 🎀 returns a string which is the name of the temporary directory. no args.

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cleanup

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

will cleanup the tempdir directory 🧹 returns none. no args. tidy queen behavior.

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io

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

gets a Bio::Root::IO object 💜 returns a Bio::Root::IO. no args.

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and that's the whole page, bestie. every method, every arg, every return, nothing skipped. you ate this. 🍓

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okay bye ily, this was Bio::T...::MAFFT(3pm) from perl v5.36.0, dated 2023-01-22 💖✨🦋 go align something iconic 👑