This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Tool: Announcing bioSyntax: Syntax highlighting for biological files

The objective of bioSyntax is to bring you closer to your data, giving you an intuitive & empathetic understanding of biology. bioSyntax integrates seamlessly with vim, less, gedit, & sublime to automatically recognize your favorite biological file formats.

For more information please visit http://biosyntax.org.

I highly recommend you to take a look at drawHelix.sh, great tool to visualize your genome. Check http://biosyntax.org/drawHelix.sh.

computational-biology
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updated by GenoMax GenoMax • written by anicet.ebou anicet.ebou

Using the https URL above is throwing up mis-configuration errors/warnings (likely related to SSL cert) in Chrome/Firefox.

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written by GenoMax GenoMax

same here (insecure connection) and security exception to be added in FF to visit the website

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written by cpad0112 cpad0112

Fix the issue by changing https by http. Thanks everybody.

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written by anicet.ebou anicet.ebou

It's surprisingly convoluted but if anyone has a git-hub page with a custom domain; adding https requires routing your DNS through CloudFlare. Fixed now :P

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written by ababaian • ababaian

3 answers

Great tool! I have a few suggestions:

  1. Maybe add support for emacs as well?
  2. source-highlight has a bunch of problems. It doesn't recognize source code all that well, and runs into a bunch of problem when using on HPC systems (it cannot find libraries easily and building for source is a headache as well). Given that supporting multiple lesspipe.sh files for piping less is not feasible, maybe the less-bam (and allied scripts) can be provided separately?
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written by Ram Ram

Heya. sam-less, vcf-less etc... are not scripts, it's an alias added to .bashrc set to run source-highlight with explicit definitions of what type of file is being input. This is because on a pipe, there is no file-extension to be recognized. If you don't want syntax-highlighting for non-biology file formats; cd /usr/share/source-highlight; sudo mv lang.map BACKUP_lang.map; touch lang.map will remove all defaults but maintain bioSyntax functionality.

I'd love to do this without source-highlight, or at least without requiring any changes to the source-highlight folder (i.e. local user configurations only). In that way source-highlight can be installed on a system by and admin once and any users who want to use syntax highlighting can just add the corresponding alias to their .bashrc files. Emacs would be nice too, and so would Nano and Atom and ... One step at a time.

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written by ababaian • ababaian

Unfortunately, anything that needs sudo doesn't work for me, as I work mostly on an HPC environment. Plus, I'm personally frustrated with source-highlight because it has way too many dependencies that cause problems when you don't have sudo. On top of that, it gets basic highlighting wrong. Lesspipe is much better IMO, as it can be run from a user dir, and adds more to the functionality of less - reading directories, archives and scanning xlsx files, for example.

I do hope an alternative to source-highlight comes up for less, as that is more important than emacs. Rarely do I edit VCF files on emacs, but I use less on them A LOT.

Thank you for this!

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written by Ram Ram

I'll look more into Lesspipe but from reading over it, I'm not sure it would be straight-forward to add syntaxes to it. From the docs though I did learn:

You can use vim less if you want to circumvent source-highlight and don't have sudo. Just ensure you have bioSyntax installed for vim and syntax enable in your .vimrc

alias vless='/usr/share/vim/vim74/macros/less.sh "$@"'

You'd have to get a little bit creative with a vimscript to also make the vcf-vless commands work. If you figure it out post it to the repo and we can incorporate it for sure.

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written by ababaian • ababaian

Will do! Thank you!

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written by Ram Ram

We (bioSyntax devs) have a very short user survey to focus future development on the file-formats and software which bioinformaticians are using. If you have a couple of minutes we'd really appreciate your input in making bioSyntax increasingly useful to our community.

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written by ababaian • ababaian

I know this is a very old thread, but I made a small related project:

https://github.com/kojix2/libbiosyntax

libbiosyntax is a small C library based on the idea of bioSyntax. It provides syntax highlighting for biological file formats such as FASTA, FASTQ, SAM, VCF, GTF, and others.

The library mainly consists of two files:

  • biosyntax.h
  • biosyntax.c

So it should be easy to embed in C projects. Bindings for other languages should also be possible.

I developed it with the help of Codex. I used the original bioSyntax source code as reference files, and improved the implementation through an iterative process. I reviewed, tested, and edited the code myself.

This is not a clean-room implementation, so I released it under GPL-3.0, following the original bioSyntax license.

Thank you to the original bioSyntax authors for creating and sharing bioSyntax. libbiosyntax could only exist because of your work.

I hope this may be useful to someone interested in lightweight syntax highlighting for biological file formats.

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written by kojix2 kojix2

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