These are chat archives for biojs/biojs

29th
Nov 2018
Sarthak Sehgal
@sarthak-sehgal
Nov 29 2018 07:52
@DennisSchwartz, asking for a functional example as an HTML file might increase the dependency on the maintainer (though it will surely make our jobs a lot easier). If we get a build file (which is easier for the maintainer since they only have to run an npm command), then we can start looking at the schema of all the components and create sort of a master schema (the old workman currently accounts for all components so it basically has that master schema). This will automate the process and all the maintainer needs to do is build their component while publishing a new version.
We can further document it so that future components follow the same schema. Revamping the workman can be a good (sub)project for GSoC 2019.
Dennis Schwartz
@DennisSchwartz
Nov 29 2018 16:55
@smsaladi That makes sense. I think you might be able to use it in the front-end as well. But looking at the docs it looks like it expects some form of stream and I’m not sure how that would work in the browser? What are you trying to do with the sequence?

@sarthak-sehgal Maybe it would, but at least it’s a very clear task. At the moment it’s very hard to understand what devs need to provide to get a working example. The documentation is out of date and not linked anywhere. And even if you find it, it’s not a very easy concept with the sniper and all that.

While saying: Give me a working example as an HTML file is pretty easy. The amount of boilerplate that will be duplicated across the examples will be minimal.

Shyam Saladi
@smsaladi
Nov 29 2018 16:58
Yeah, that's where I got confused too ... how to work with a stream in the browser. The user provides a sequence(s) in fasta format, I just need to handle/calculated on each separately and return the calculation to the user. Is there another package that might be better suited for this sort of thing? I was just thinking that it might be better to use a package than rolling my own parser (maybe not?). (Sorry in advance for these really simple questions)
Dennis Schwartz
@DennisSchwartz
Nov 29 2018 17:00
No no those are good questions haha. I’m not which packages are around but I’ll have a quick look. So basically you would like to get all the sequencees of the Fasta separately?
I think this one could work:
https://www.npmjs.com/package/biojs-io-fasta
Shyam Saladi
@smsaladi
Nov 29 2018 17:03
This looks perfect, thank you!
Dennis Schwartz
@DennisSchwartz
Nov 29 2018 17:09
You’re welcome :)