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

💖 Bio::Tools::Run::TribeMCL 💖

okay bestie, gather round, because today we're talking about Bio::Tools::Run::TribeMCL — the Perl module that does the Markov method for CLustering proteins ✨ Like, it takes your sad little pile of protein similarities and hands you back actual protein families. Main character energy fr fr 🫶

This page lives in the User Contributed Perl Documentation, and the whole vibe is "I want my proteins grouped and I want it now". Let's go 💅

---

✨ NAME ✨

Bio::Tools::Run::TribeMCL — Markov method for CLustering proteins 🌸

---

🦋 SYNOPSIS 🦋

use Bio::Tools::Run::TribeMCL;
use Bio::SearchIO;

# 3 methods to input the blast results

# straight forward raw blast output (NCBI or WU-BLAST)
my @params = ('inputtype'=>'blastfile');

# OR

# markov program format
# protein_id1 protein_id2 evalue_magnitude evalue_factor
# for example:
# proteins ENSP00000257547  and ENSP00000261659
# with a blast score evalue of 1e-50
# and proteins O42187 and ENSP00000257547
# with a blast score evalue of 1e-119
# entry would be

my @array  = [[qw(ENSP00000257547 ENSP00000261659 1 50)],
              [qw(O42187 ENSP00000257547 1 119)]];
my @params = ('pairs'=>\@array,I=>'2.0');

# OR

# pass in a searchio object
# slowest of the 3 methods as it does more rigourous parsing
# than required for us here

my $sio = Bio::SearchIO->new(-format=>'blast',
                             -file=>'blast.out');
my @params=('inputtype'=>'searchio',I=>'2.0');

# you can specify the path to the executable manually in the following way
my @params=('inputtype'=>'blastfile',I=>'2.0',
            'mcl'=>'/home/shawn/software/mcl-02-150/src/shmcl/mcl',
            'matrix'=>'/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix');
my $fact = Bio::Tools::Run::TribeMCL->new(@params);

# OR

$fact->matrix_executable('/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix');
$fact->mcl_executable('/home/shawn/software/mcl-02-150/src/shmcl/mcl');

# to run

my $fact = Bio::Tools::Run::TribeMCL->new(@params);

# Run the program
# returns an array reference to clusters where members are the ids
# for example :2 clusters with 3 members per cluster:
#  $fam = [ [mem1 mem2 mem3],[mem1 mem2 mem3]]

# pass in either the blastfile path/searchio obj/the array ref to scores
my $fam = $fact->run($sio);

# print out your clusters

for (my $i = 0; $i <scalar(@{$fam}); $i++){
  print "Cluster $i \t ".scalar(@{$fam->[$i]})." members\n";
  foreach my $member (@{$fam->[$i]}){
    print "\t$member\n";
  }
}

---

🌈 DESCRIPTION 🌈

So here's the tea ☕ TribeMCL is a method for clustering proteins into related groups, and those groups are called 'protein families' 👑 How does it do it? It analyses similarity patterns between proteins in a given dataset, and then uses those patterns to assign proteins into related groups. And bestie, in many cases, proteins sitting in the same protein family will have similar functional properties. Iconic behavior, honestly 💅

TribeMCL uses a novel clustering method (Markov Clustering, aka MCL) which solves problems which normally hinder protein sequence clustering. Slay 🔥

Reference:

Enright A.J., Van Dongen S., Ouzounis C.A; Nucleic Acids
Res. 30(7):1575-1584 (2002)

⚠️ heads up bestie — you will need tribe-matrix (the program used to generate the matrix for input into mcl) and mcl (the clustering software) available at: http://www.ebi.ac.uk/research/cgg/tribe/ or http://micans.org/mcl/.

Future Work in this module: Port the tribe-matrix program into perl so that we can enable have a SearchIO kinda module for reading and writing mcl data format 🧚 (yes, that's the dream, no cap)

---

🎀 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 🫶

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 🙏

🐛 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/

---

👑 AUTHOR - Shawn Hoon 👑

Email shawnh@fugu-sg.org 💌

---

💜 APPENDIX 💜

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_" 🫣

🧚 mcl_executable

• Title: mcl_executable
• Usage: $self->mcl_executable()
• Function: get set for path to mcl executable
• Returns: String or undef if not installed
• Args:
  • [optional] string of path to executable
  • [optional] boolean to warn on missing executable status

🧚 matrix_executable

• Title: matrix_executable
• Usage: $self->matrix_executable()
• Function: get set for path to tribe-matrix executable
• Returns: String or undef if not installed
• Args:
  • [optional] string of path to executable
  • [optional] boolean to warn on missing executable status

🧚 run

• Title: run
• Usage: $self->run()
• Function: runs the clustering
• Returns: Array Ref of clustered Ids
• Args: (none)

🧚 _run_mcl

• Title: _run_mcl
• Usage: $self->_run_mcl()
• Function: internal function for running the mcl program
• Returns: Array Ref of clustered Ids
• Args: Index_file name, matrix input file name

🧚 _run_matrix

• Title: _run_matrix
• Usage: $self->_run_matrix()
• Function: internal function for running the tribe-matrix program
• Returns: index filepath and matrix file path
• Args: filepath of parsed ids and scores

🧚 _setup_input

• Title: _setup_input
• Usage: $self->_setup_input()
• Function: internal function for running setting up the inputs needed for running mcl
• Returns: filepath of parsed ids and scores
• Args: (none)

🧚 _get_from_hsp

• Title: _get_from_hsp
• Usage: $self->_get_from_hsp()
• Function: internal function for getting blast scores from hsp
• Returns: array ref to ids and score [protein1 protein2 magnitude factor]
• Args: Bio::Search::HSP::GenericHSP

🧚 _get_from_searchio

• Title: _get_from_searchio
• Usage: $self->_get_from_searchio()
• Function: internal function for parsing blast scores from searchio object
• Returns: array ref to ids and score [protein1 protein2 magnitude factor]
• Args: Bio::Tools::SearchIO

🧚 _parse_blastfile

• Title: _parse_blastfile
• Usage: $self->_parse_blastfile()
• Function: internal function for quickly parsing blast evalue scores from raw blast output file
• Returns: array ref to ids and score [protein1 protein2 magnitude factor]
• Args: file path

🧚 _parse_mcl

• Title: _parse_mcl
• Usage: $self->_parse_mcl()
• Function: internal function for quickly parsing mcl output and generating the array of clusters
• Returns: Array Ref of clustered Ids
• Args: index file path, mcl output file path

---

and that's the whole page bestie 💖 this one shipped as perl v5.36.0, dated 2023-01-22, and it's the Bio::T...ribeMCL(3pm) page from the User Contributed Perl Documentation — go cluster something pretty ✨🦋🎀