BioJulia/BioSequences.jl

Ben J. Ward

@BenJWard

Is that because it needs some special support from the interpreter?

Jakob Nybo Nissen

@jakobnissen

Yes, at least according to this https://discourse.julialang.org/t/generalizing-bounds-checking/4704

Ben J. Ward

@BenJWard

Maybe we can do it with an API then

Passing Val{true} is described

Jakob Nybo Nissen

@jakobnissen

I'd just export unsafe_setindex!.

Ben J. Ward

@BenJWard

or we could simply have unsafe_* version of the methods that edit any sequences.

Jakob Nybo Nissen

@jakobnissen

Yep, that's neater I think. Probably add a small docstring saying that it skips all boundschecks and copy-on-write checks :)

Ben J. Ward

@BenJWard

I think this is smart

I'll make that the next PR after the current one then!

Jakob Nybo Nissen

@jakobnissen

Hm, what's the intended use of CharSequence? It seems like it's a complicated String.

Ben J. Ward

@BenJWard

Pretty much! :laughing:

I think it's just to show that with BioSequences you could store any element type, using an alphabet.

I think each char is stored in 8 bits, and so if you were doing bitops you could do things more quickly... what kind of things I've no idea

CharSequences are also mutable which String is not

But really it's something that is there, but isn't really used much right now.

I do envisage other alphabets in the future to store, for example a sequence of SNPs and that sort of thing as BioSequences would let you do that, but again there's no need or call for it right now.

Ben J. Ward

@BenJWard

@jakobnissen Do you think there's any merit it seperating the process into three stages? - boundscheck -> cowcheck -> unsafe opertation, or do you think two steps of bounds & cow-check -> unsafe operation is enough?

Jakob Nybo Nissen

@jakobnissen

I don't think the user cares that much about which internal checks BioSequences are doing. They probably just want a safe option (default) and an unsafe but fast option (where the documentation clearly states exactly which precautions they should take). However, I don't think it'sa good idea to make the COW-check parts of the bounds heck so it can be skipped with @inbounds, because the user might th

might reasonably assume that @inbounds only skill skipsa boundscheck and so might use it wrong

One of the best things about the COW-principle is that the user benefits without even having to know it's there.

Jakob Nybo Nissen

@jakobnissen

Just a heads-up: AminoAcidAlphabet()[1] doesn't work currently on the v2 branch. You need to convert i - 1 to UInt8 first. Same with the NucleicAcidAlphabet{4} subtypes.

Ben J. Ward

@BenJWard

Good catch!

Jakob Nybo Nissen

@jakobnissen

With the code coverage bot currently being untrustworthy, is there any way to figure out how many lines in your code you've written tests for?

Jakob Nybo Nissen

@jakobnissen

@BenJWard I get deprecation warning when testing BioSequences due to a function in Twiddle:
┌ Warning: repeatbyte is deprecated, use repeatpattern instead
│ caller = count_01_bitpairs at counting.jl:79 [inlined]
└ @ Core ~/.julia/packages/Twiddle/MbfXo/src/counting.jl:79

Ben J. Ward

@BenJWard

@jakobnissen Yes I'm aware of that one, I think it's my fault, it's something in the bit-parallel site counting code I developed last year. I found a way to make some generic methods for bit-twiddling that work for all Unsigned sizes, with zero cost to performance, so I put them in Twiddle and also renamed some of them. I'll make a PR fixing this.

Guillermo Luque

@gluque

Hello there! I've installed Julia 1.3.0 but when installing BioSequences, it uses the 1.1 instead of the 2.0 version, do you know how to "force" the 2.0 version when installing?

Ben J. Ward

@BenJWard

@gluque Hiya,

Have you added the "BioJulia package registry" to your julia setup?

registry add https://github.com/BioJulia/BioJuliaRegistry.git

v2.0 of BioSequences, FASTX, Pseudoseq, and the newer packages (or newer versions of old packages) are being released through the "BioJulia package registry" now instead of the "General" registry.

Guillermo Luque

@gluque

Hello @BenJWard Thanks! It is working after updating the registry.

Ciarán O'Mara

@CiaranOMara

@BenJWard and @jakobnissen, have you guys seen https://github.com/tkf/BenchmarkCI.jl ?

Ghost

@ghost~5ede2c26d73408ce4fe64346

Hello! I understand that I should use FASTX for parsing FASTA files but how do I convert FASTX's FASTA records into a BioSequences type? I'm having a hard time finding this in the documentation.

Ghost

@ghost~5ede2c26d73408ce4fe64346

I found that I can use BioSequences.sequence(FASTX.FASTA.Record) to do this, in case anyone else is wondering the same thing.

Ben J. Ward

@BenJWard

Yep that's right. In any upcoming releases this method may be deprecated in favour of getting the user to simply use a constructor e.g. LongSequence{DNAAlphabet{2}}(record).

Ghost

@ghost~5ede2c26d73408ce4fe64346

Another question: I have Julia installed on two separate computers. On my Linux machine, I have the latest version of BioSequences.jl but my MacBook has v1.1.0. I am running update but it doesn't do anything. I have Julia v1.4 installed on both machines. I am updating from the general registry on both machines and I shouldn't have to add the BioJulia registry anymore if I understand things correctly.

Ghost

@ghost~5ede2c26d73408ce4fe64346

Solved. I removed ~/.julia/registries/General, then I ran ]registry update General, and then I reinstalled all of my bio-related packages. I think the problem was that BioTools.jl depends on an older version of BioSequences.jl. Sorry for spamming the chat!

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