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

✨ Bio::T...::Amap(3pm) ✨

hey bestie 💖 so this page comes to you straight from the User Contributed Perl Documentation, and it's all about an object that runs the Amap program for you. buckle up, it's giving bioinformatics but make it cute 🌸

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💅 NAME 💅

Bio::Tools::Run::Alignment::Amap — an object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Amap (2.0) program 🦋

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🌈 SYNOPSIS 🌈

okay so here's the vibe. you build a factory, you hand it sequences, you get an alignment back. slay.

# Build a muscle alignment factory
$factory = Bio::Tools::Run::Alignment::Amap->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 amap with training, try something like:

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

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

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🧚 DESCRIPTION 🧚

so Amap uses a Sequence Annealing algorithm, which is an incremental method for building multiple alignments. it's giving "slow and steady wins the race" and honestly? iconic. you can get it and see information about it at this URL: http://bio.math.berkeley.edu/amap/

🔍 Helping the module find your executable 🔍

FIXME: Amap uses the same parameters as Probcons, plus a few others. I haven't had time to check all the changes from the Probcons.pm runnable. Feel free to do it.

no cap, bestie — you have to let Amap find the amap program. there are (at least) three ways to do this:

1. make sure the amap executable is in your path (i.e. 'which amap' returns a valid program 👑)
2. define an environmental variable AMAPDIR which points to a directory containing the amap app:

in bash:

export AMAPDIR=/home/progs/amap   or

in csh/tcsh:

setenv AMAPDIR /home/progs/amap

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

BEGIN {$ENV{AMAPDIR} = '/home/progs/amap'; }
use Bio::Tools::Run::Alignment::Amap;

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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 one of the Bioperl mailing lists. 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. so 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 foo@bar.com

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🎀 APPENDIX 🎀

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk, those are the ones you don't touch unless you know exactly 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:

new

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

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

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.

like bestie, it WILL throw hands (an exception) if you feed it something it doesn't understand 💀

_run

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

_setinput

• Title: _setinput
• Usage: Internal function, not to be called directly
• Function: Create input file for amap program
• Example:
• Returns: name of file containing amap 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 amap program
• Example:
• Returns: parameter string to be passed to amap 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 🌟

these ones are inherited from the base wrapper, and they're all lowkey essential 🫶

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 = $amap->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: $amap->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...::Amap(3pm) in the User Contributed Perl Documentation. go forth and align, you absolute main character 👑🌈