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

💖 NAME 💖

Bio::Tools::Run::Gerp — it's the wrapper for GERP, bestie. That's the whole vibe. (The page itself is filed under the manual name Bio::T...::Gerp, in case you were wondering why the header looked like that. User contributed Perl documentation, iconic behavior.)

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✨ SYNOPSIS ✨

Okay so first you gotta pull in the right module — heads up, it lives under the Phylo namespace:

use Bio::Tools::Run::Phylo::Gerp;

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

# Run Gerp with an alignment and tree file
my $parser = $factory->run($alignfilename, $treefilename);

# or with alignment object and tree object (which needs branch lengths)
$parser = $factory->run($bio_simplalign, $bio_tree_tree);

# (mixtures of the above are possible)

# look at the results
while (my $feat = $parser->next_result) {
  my $start = $feat->start;
  my $end = $feat->end;
  my $rs_score = $feat->score;
  my $p_value = ($feat->annotation->get_Annotations('p-value'))[0]->value;
}

No cap, you can mix and match the file/object thing. The factory does not care. 🫶

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🌸 DESCRIPTION 🌸

So this is a wrapper for running the GERP (v2) programs gerpcol and gerpelem, written by Eugene Davydov (originally Gregory M. Cooper et al.). Deets live here: http://mendel.stanford.edu/sidowlab/. GERP is the moment for phylogenetic footprinting / shadowing — it goes and finds constrained elements in multiple alignments. Literally its whole job.

You can just throw normal gerpcol/gerpelem command-line arguments at new(), like $factory->new(-e => 0.05), or call arg-named methods instead, like $factory->e(0.05). Both work, pick your fighter. The filename-related args (t, f, x) are handled internally by the run() method, so don't worry about those. Lowkey important: this wrapper currently only supports running GERP on a single alignment at a time — so F isn't used at all, and multiple fs aren't possible either. One alignment. That's the rule. 💅

Also you'll need to let this GERP wrapper actually find the GERP executables. There's (at least) three ways to do that:

1. Make sure gerpcol and gerpelem are in your path.
2. Define an environmental variable GERPDIR which is a directory which contains the GERP executables. In bash:

export GERPDIR=/home/username/gerp/

In csh/tcsh:

setenv GERPDIR /home/username/gerp

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

BEGIN { $ENV{GERPDIR} = '/home/username/gerp/' }
use Bio::Tools::Run::Phylo::Gerp;

Pick whichever one speaks to you. 🦋

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🎀 FEEDBACK 🎀

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules, fr fr. Send your comments and suggestions preferably to the Bioperl mailing list. 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 so many experienced and reponsive experts who will be able look at the problem and quickly address it. If at all possible, please include a thorough description of the problem with code and data examples. Give them the full picture bestie, they'll love you for it. 💜

🐛 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 Bidu 👑

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 _. (You know the drill — if it starts with an underscore, it's giving backstage-pass energy, don't touch it unless you know 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    : None

⭐ new

Title   : new
Usage   : $factory = Bio::Tools::Run::Phylo::Gerp->new()
Function: creates a new GERP factory
Returns : Bio::Tools::Run::Phylo::Gerp
Args    : Most options understood by GERP can be supplied as key =>
          value pairs.

          These options can NOT be used with this wrapper:
          h, t, f, F and x

Bestie, listen: h, t, f, F and x are off-limits with this wrapper. Do not try it. It's not gonna go how you want. 🙈

⭐ run

Title   : run
Usage   : $parser = $factory->run($align_file, $tree_file);
          -or-
          $parser = $factory->run($align_object, $tree_object);
Function: Runs GERP on an alignment.
Returns : Bio::Tools::Phylo::Gerp parser object, containing the results
Args    : The first argument represents an alignment, the second argument
          a phylogenetic tree with branch lengths.
          The alignment can be provided as a MAF format alignment
          filename, or a Bio::Align::AlignI compliant object (eg. a
          Bio::SimpleAlign).
          The species tree can be provided as a newick format tree filename
          or a Bio::Tree::TreeI compliant object.

          In all cases, the alignment sequence names must correspond to node
          ids in the tree. Multi-word species names should have the
          spaces replaced with underscores (eg. Homo_sapiens)

Okay so the naming thing is not negotiable — the alignment sequence names must line up with the node ids in the tree, and if a species name has multiple words you swap the spaces for underscores, like Homo_sapiens. Do that and you're slaying. Don't do that and you're gonna have a bad time. 😭

⭐ _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    : none

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Okay that's the whole page bestie, you're fully caught up, main character energy achieved. This one's running on perl v5.36.0 and it was dated 2023-01-22 — so go forth, run your GERP, find those constrained elements, and remember: single alignment at a time. Periodt. 🎀✨