Hi to all,

I rarely advertise my humble blog directly, but I believe this is worth it. I also need your help for "quality control".

I work with nucleotide and amino acid sequences and FASTA is among the most commonly used text file formats for biological sequences. I wanted my text editor (medit) to be able to display colour code for the nucleotides and/or amino acid residues. Long story short, I ended up making my own fasta.lang file and an accompanying modified Tango style, which I called BioTango.

here's the link to my blog post:

https://slackalaxy.com/2017/06/25/fa...tax-highlight/

I don't have experience with lang or xml files, so may I kindly ask you to check if I did thinbgs correctly? Any suggestions are welcome. This is a preview of what I am talking about:

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I hate to break this to you, but you're probably the only one with an interest in Slackware and research into nucleotide and amino acid sequences. I applaud you for using a sensible OS for your work, but I think you're better off finding a forum where your colleagues are more likely to give an informed opinion of what you are asking. There's got to be another person using Linux and works in your field. Just a thought.

Happy Slacking!

1 members found this post helpful.

Ah, I already figured this out myself...

I have seen people here discussing some of the sequence analysis/assembly tools that I maintain at SBo, though. Slackware's forum at LQ is probably the only forum that I participate in. I will search however if someone needed this syntax highlight and let them know it exists.

you are right, I will therefore mark the thread as SOLVED.

well, you kinda make it sound as if I am some rare specimen in the otherwise homogeneous Linux world...

I also work in the same field, now we are at least 2...

However, I do not analyze FASTA files for the moment but PLINK or VCF-files. I also do not work with XML so, cannot help you here m8.

1 members found this post helpful.

Your implication that you are not alone is probably right on, but over the years I've found that there are some unique combinations of talents and interests that combine in the same person, so therefore sometimes it can be difficult to seek help when the problem overlaps two seemingly unrelated areas. However in your case, there's at least one (Bindestreck) who works in your field, so that's a start; a small one (he can't help you in your request), but still, there's hope.

Great! shall we make a count, like how many Slackware users work in the field of biology? :P

well, yes of course... I guess fasta (or any _plain_ sequence format file) is just the start. I realy do not do much with sequence files in my text editor, apart from using them as input for anoher program. I just thought it would be neat if I could see the nucleotides or amino acids in colour... I am thinking that I could make another syntax for, say, codon alignments that would colour codons based on (surprise, surprise) the amino acid they code and also highlight start and stop codons... but not right now. Thanks for joining. I do not feel so alone :P

2 members found this post helpful.