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

💖 Bio::Tools::Run::Alignment::Probcons 💖

Hiii bestie, welcome to the User Contributed Perl Documentation page (that's the 3pm manual, iykyk) for Bio::Tools::Run::Alignment::Probcons. Grab a strawberry 🍓 and let's get into it.

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✨ NAME ✨

Bio::Tools::Run::Alignment::Probcons — it's giving object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Probcons program. That's the whole vibe. 🧬

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✨ SYNOPSIS ✨

Okay so, here's how you actually use it, no cap:

# Build a muscle alignment factory
$factory = Bio::Tools::Run::Alignment::Probcons->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.

#To run probcons with training, try something like:

#First round to generate train.params
$factory = Bio::Tools::Run::Alignment::Probcons->new
    (
     'iterative-refinement'  => '1000',
     'consistency'   => '5',
     'pre-training' => '20',
     'emissions' => '',
     'verbose' => '',
     'train'   => "$dir/$subdir/$outdir/train.params",
    );
$factory->outfile_name("$dir/$subdir/$outdir/train.params");

#Second round to use train.params to get a high qual alignment

$seq_array_ref = \@seq_array;
$aln = $factory->align($seq_array_ref);
$aln = '';
$factory = '';

$factory = Bio::Tools::Run::Alignment::Probcons->new
    (
     'iterative-refinement'  => '1000',
     'consistency'   => '5',
     'pre-training' => '20',
     'verbose' => '',
     'paramfile'   => "$dir/$subdir/$outdir/train.params",
    );
$factory->outfile_name("$dir/$subdir/$outdir/outfile.afa");
$aln = $factory->align($seq_array_ref);

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✨ DESCRIPTION ✨

Probcons is a Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences. Iconic. You can grab it and read all about it right here: http://probcons.stanford.edu/ 🌐

🧭 Helping the module find your executable

Bestie, you have to let this module find the probcons program. There are (at least) three ways to make that happen, and honestly pick your fighter:

1. Just make sure the probcons executable is in your path (like, which probcons returns a valid program — that's the vibe check ✅).
2. Define an environmental variable PROBCONSDIR that points to a directory containing the probcons app:

In bash:

export PROBCONSDIR=/home/progs/probcons   or

In csh/tcsh:

setenv PROBCONSDIR /home/progs/probcons

3. Include a definition of an environmental variable PROBCONSDIR in every script that will:

BEGIN {$ENV{PROBCONSDIR} = '/home/progs/probcons'; }
use Bio::Tools::Run::Alignment::Probcons;

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✨ FEEDBACK ✨

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. So 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. There are lots of experienced and responsive experts who will be able to look at the problem and quickly address it. And please include a thorough description of the problem with code and data examples if at all possible — the more deets the better, fr fr. 🙏

🐛 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 - Jason Stajich 🌟

Email: jason-at-bioperl-dot-org

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✨ APPENDIX ✨

The rest of the documentation details each of the object methods. Heads up: internal methods are usually preceded with a _ — so if you see that underscore, mind your business, it's internal 💅

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 $probcons = Bio::Tools::Run::Alignment::Probcons->new();
• Function: Constructor
• Returns: Bio::Tools::Run::Alignment::Probcons
• 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() < 1.8
• Function: Determine the version number of the program
• Example: (blank in the original, it's just vibing 🫥)
• 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.

⚠️ It throws an exception if the argument is not either a string (like a filename) or a reference to an array of Bio::Seq objects. If the argument is a string, it throws an exception if the file corresponding to that string name can not be found. And if the argument is a Bio::Seq array, it throws an exception if there are less than two sequence objects in the array. So don't try it. 💀

_run

• Title: _run
• Usage: Internal function, not to be called directly
• Function: makes actual system call to probcons program
• Example: (blank, as the original says 😌)
• Returns: nothing; probcons 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 probcons

_setinput

• Title: _setinput
• Usage: Internal function, not to be called directly
• Function: Create input file for probcons program
• Example: (blank 🫥)
• Returns: name of file containing probcons data input AND (yes bestie, the original sentence literally trails off right there with "AND" — we keep it exactly as-is, no notes 💀)
• Args: Arrayref of Seqs or input file name

_setparams

• Title: _setparams
• Usage: Internal function, not to be called directly
• Function: Create parameter inputs for probcons program
• Example: (blank 🫥)
• Returns: parameter string to be passed to probcons 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

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: (the original leaves this one blank, so we leave it blank too 🫶)
• Returns: value of save_tempfiles
• Args: newvalue (optional)

outfile_name

• Title: outfile_name
• Usage: my $outfile = $probcons->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: $probcons->cleanup();
• Function: Will cleanup the tempdir directory
• Returns: none
• Args: none

io

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

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And that's the whole page, bestie! 🎀 This lil masterpiece is perl v5.36.0, dated 2023-01-22, and it lives under the Bio::T...obcons(3pm) banner. Slay, periodt. 💅✨