BioPerl(3pm)

💖 BioPerl 💖

okay bestie, sit down, hydrate, because we're about to talk about BioPerl — literally Perl modules for biology, and honestly? iconic. 🧬✨

The manual name is BioPerl(3pm), so if you ever need to yell at your terminal for it, that's the name you scream.

---

✨ VERSION ✨

version 1.7.8 — that's the one, that's the vibe. 🎀

---

🌸 SYNOPSIS 🌸

If you're new to BioPerl (welcome, baby BioPerl-er 🫶), you should start by reading the BioPerl HOWTO's:

<http://bioperl.org/howtos/index.html>

📚 References for Individual Modules

So, for ease of maintenance and coordination amongst contributors, the BioPerl code is maintained in a modular form — and so is the documentation. Which means: to read the docs for individual modules, you use perldoc. Like, for real, literally:

"perldoc Bio::Seq"

and boom 💥 you get the documentation for the Bio::Seq object. Slay.

---

🦋 DESCRIPTION 🦋

BioPerl is the product of a community effort to produce Perl code that's useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. And here's the part that's lowkey the best: these objects don't just do what they're advertised to do in the documentation — they also interact. Alignment objects are made from the Sequence objects, Sequence objects have access to Annotation and SeqFeature objects and databases, Blast objects can be converted to Alignment objects, and so on and so on. Which means the objects give you a coordinated and extensible framework to do computational biology. Main character framework energy, honestly. 👑

BioPerl development focuses on Perl classes, aka code used to create objects representing biological entities. There are scripts provided in the scripts/ and examples/ directories, but — real talk — scripts are not the main focus of the BioPerl developers. And of course, since the objects do most of the hard work for you, all you have to do is combine a number of objects together sensibly to make useful scripts. Easy? Easy. 💅

The intent of the BioPerl development effort is to make reusable tools that aid people in creating their own sites or job-specific applications.

Also, the BioPerl website at <http://bioperl.org> tries to maintain links and archives of standalone bio-related Perl tools that aren't affiliated or related to the core BioPerl effort. Check the site for useful code ideas, and contribute your own if you can! 🌈

---

🎀 INSTALLATION 🎀

The BioPerl modules are distributed as a tar file that expands into a standard perl CPAN distribution. Detailed installation directions live in the distribution INSTALL file. Installing on windows using ActiveState Perl is covered in the INSTALL.WIN file. And ngl, we highly suggest reading the installation instructions on the BioPerl website:

<http://bioperl.org/INSTALL.html>

Heads up bestie: only the following are supported at this time with the current API: - BioPerl-db - BioPerl-network - BioPerl-run - BioPerl-pedigree - Bio::Graphics

---

🌟 GETTING STARTED 🌟

The distribution scripts/ directory has working scripts for use with BioPerl — and check the self-described examples/ directory too. And you are more than welcome to contribute your script! fr fr, we want it. 🫶

If you've installed BioPerl in the standard way, as detailed in the INSTALL in the distribution, these scripts should work by just running them. That's it. That's the whole thing. ✨

---

💜 GETTING INVOLVED 💜

BioPerl is a completely open community of developers. We are not funded and we don't have a mission statement. We encourage collaborative code, in particular in Perl. You can help us in many different ways — from just a simple statement about how you've used BioPerl, to doing something interesting, all the way to contributing a whole new object hierarchy. See <http://bioperl.org> for more information. Here are some ways of helping us:

🙋 Asking questions and telling us you used it

We are very interested to hear how you experienced using BioPerl. Did it install cleanly? Did you understand the documentation? Could you get the objects to do what you wanted them to do? If BioPerl was useless we want to know why, and if it was great — that too. Post a message to bioperl-l@bioperl.org, the BioPerl mailing list, where all the developers are. 📬

Only by getting people's feedback do we know whether we are providing anything useful. So like, your feedback is the vibe check we need.

📝 Writing a script that uses it

By writing a good script that uses BioPerl you both show that BioPerl is useful and probably save someone elsewhere from writing it. If you contribute it to the 'script central' at <http://bioperl.org> then other people can view and use it. Don't be nervous if you've never done this sort of work — advice is freely given and all are welcome! 🥹

🐛 Find bugs!

We know that there are bugs in this code. (Not me admitting it, but okay, we're being honest.) If you find something which you're pretty sure is a problem, post a bug report using our Bugzilla tracking system:

<https://github.com/bioperl/bioperl-live/issues>

Please read the main bug tracking (<http://www.bioperl.org/articles/Bugs.html>) for an overview of what we expect in a bug report. Specifically, having a code and data example where appropriate helps tremendously. And we gladly accept all patches after a quick code review. 💀➡️🔥

💡 Suggest new functionality

You can suggest areas where the objects are not ideally written and could be done better. The best way is to find the main developer of the module (each module was written principally by one person, except for Seq.pm). Talk to him or her and suggest changes. ☕

🧚 Make your own objects

If you can make a useful object we will happily include it into the core. Probably you will want to read a lot of the documentation in Bio::Root::Root and talk to people on the BioPerl mailing list, bioperl-l@bioperl.org. 👑

📖 Writing documentation

We appreciate good documentation. It's what tells the world what's in BioPerl, it's what instructs the user, it's what describes the rationale and inner workings of the package. Feel free to contribute. 💖

---

👑 ACKNOWLEDGEMENTS 👑

For a more detailed history of the BioPerl project, we recommend the History of BioPerl:

<http://bioperl.org/articles/History_of_BioPerl.html>

---

💌 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 the Bioperl mailing list. Your participation is much appreciated. 🫶

  bioperl-l@bioperl.org               - General discussion
  https://bioperl.org/Support.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. (Yes, directly. Don't do it. 🙈) 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 of the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

---

✍️ AUTHOR ✍️

See the individual modules for their authors.

---

©️ COPYRIGHT ©️

This software is copyright (c) by many people (see the individual modules for their copyright holders).

This software is available under the same terms as the perl 5 programming language system itself.

---

and that's the whole page bestie!! 🎀✨ this was perl v5.32.1, dated 2021-08-15, and it's the BioPerl(3pm) manual page — go forth and object-orient your biology, you absolute legend 💅💖🧬