Announcing bioSyntax: Syntax highlighting for biological files

News: Announcing bioSyntax: Syntax highlighting for biological files

3.0 years ago by

anicet.ebou • 160 wrote:

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 informations 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 news bioinformatics • 1.5k views

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modified 2.7 years ago by ababaian • 50 • written 3.0 years ago by anicet.ebou • 160

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

ADD REPLY • link written 3.0 years ago by GenoMax ♦ 94k

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

ADD REPLY • link modified 3.0 years ago • written 3.0 years ago by cpad0112 ♦ 14k

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

ADD REPLY • link modified 3.0 years ago • written 3.0 years ago by anicet.ebou • 160

Can't you use let's encrypt/certbot to add free https support ? https://certbot.eff.org/

ADD REPLY • link written 3.0 years ago by Raony Guimarães • 1.1k

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

ADD REPLY • link written 3.0 years ago by ababaian • 50

3.0 years ago by

_r_am ♦ 32k

Baylor College of Medicine, Houston, TX

_r_am ♦ 32k wrote:

Great tool! I have a few suggestions:

Maybe add support for emacs as well?
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?

ADD COMMENT • link modified 3.0 years ago • written 3.0 years ago by _r_am ♦ 32k

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.

ADD REPLY • link written 3.0 years ago by ababaian • 50

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!

ADD REPLY • link written 3.0 years ago by _r_am ♦ 32k

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.

ADD REPLY • link written 3.0 years ago by ababaian • 50

Will do! Thank you!

ADD REPLY • link written 3.0 years ago by _r_am ♦ 32k

2.7 years ago by

ababaian • 50

Vancouver, BC

ababaian • 50 wrote:

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.

ADD COMMENT • link written 2.7 years ago by ababaian • 50

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