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sharkdp / bat

A cat(1) clone with wings.
Apache License 2.0
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Highlighting for bioinformatics #2806

Open TullyMonster opened 6 months ago

TullyMonster commented 6 months ago

To be able to extend the file formats commonly used in bioinformatics, I used BioSyntax.

After following these steps Adding new syntaxes / language definitions, but it doesn't seem to work. image

Test from WSL Ubuntu.

I would venture to speculate that compatibility is to blame, because of the bioSyntax-based configuration, there is a dedicated tool: https://github.com/bioSyntax/bioSyntax-sublime

But I prefer bat to it, obstinately. I don't know much about the technical details of bat, and I hope to address the needs of many bioinformatics researchers to help me solve this problem. The noblest thanks go to everyone who cares about it.

keith-hall commented 6 months ago

Hi, it looks like the syntax definition is using extremely non-standard scopes. Probably you have to use one of the colour schemes from that package also.

TullyMonster commented 6 months ago

Hi, it looks like the syntax definition is using extremely non-standard scopes. Probably you have to use one of the colour schemes from that package also.

Thx, if I know the specific .sublime-syntax file such as fasta.sublime-syntax, how can I determine its standardization and make amendments?

keith-hall commented 6 months ago

scopes like ntA are completely arbitrary and don't match anything in http://www.sublimetext.com/docs/scope_naming.html

I count about 17 unique scopes in that fasta syntax definition, and I guess there's no way to use semantic/"correct" scopes, but just to try mapping some scopes which color schemes generally target/color distinguishably.

TullyMonster commented 6 months ago

scopes like ntA are completely arbitrary and don't match anything in http://www.sublimetext.com/docs/scope_naming.html

I count about 17 unique scopes in that fasta syntax definition, and I guess there's no way to use semantic/"correct" scopes, but just to try mapping some scopes which color schemes generally target/color distinguishably.

Thanks for your reply. So in that case, are there any proposed tools for highlighting bioinformatics data or is bat planning to consider compatibility with them? ❤️