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Mateusz Kaduk
@matkad_gitlab
Whats the status of BioJulia now? I am trying to use Bio.Seq to read fastq files, but it seems its not working with 1.0.x
there also seems to be BioSequences package, is there a reason why they're not under the same umbrella but separate? :)
Joe Greener
@jgreener64
Bio.jl is an umbrella package that collects and re-exports other packages from the BioJulia ecosystem, e.g. Bio.Seq is just the BioSequences package.
Most of the individual packages work and can be used now on v0.7/v1.0.x.
Bio.jl still needs a bit of work, or perhaps just a release tagged. I think @BenJWard was working on that but of course PRs are very welcome.
Mateusz Kaduk
@matkad_gitlab
@jgreener64 thanks Joe, I have another question, I am using Juno/Emacs and in both cases I dont see completion for FASTQ modules inside BioSequences. Is that expected? Do you know IDE that can show available modules/functions from packages?
Joe Greener
@jgreener64
I think the Julia plugin for VScode can do something like this, see https://github.com/JuliaEditorSupport/julia-vscode/wiki/IntelliSense.
You might also get more info on the Julia Gitter, the Julia Slack, or Discourse.
Christopher Rackauckas
@ChrisRackauckas
apropos("PackageName")
Mateusz Kaduk
@mateusz-kaduk_gitlab
@BenJWard Hey Ben, is there a reason why Pkg.clone("https://github.com/BioJulia/Bio.jl.git") is fixed to 1.0.0 version, would it be possible to relax requirement a bit to have it 1.0.x ? :)
When I try to install on 1.0.2 I get something like this
restricted to versions 1.0.0 by an explicit requirement — no versions left
Thanks! :)
Scott McCain
@jspmccain
Hey! Just wondering if anybody here is using Julia for proteomics?
kdyrhage
@kdyrhage
@jspmccain To some extent
Ben J. Ward
@BenJWard
Last time I had a go at testing Bio.jl, with the aim of tagging a release, BioServices.jl was not passing all tests. I'm not sure if this was fixed yet, I'll try again (I test locally with Bio.jl because of the number of packages it has to test means travis stops).
Ben J. Ward
@BenJWard
@/all Can I please ask everyone that any conversations and questions that are generic in nature and not specific to the BioJulia/Bio.jl exactly, take place over at https://gitter.im/BioJulia/General instead.
@/all I'm sutting down the Discord server in favour of the creation of a General Gitter room, for general Q&A and chat, and then a series of package specific rooms for very detailed Q's about a package, and dev chat. The Discord server has not made my life easier as I hoped it might.
@/all Thank you!
Ivan Dorna
@dorvan
@/all Hello
we are a team who wants to move from R(xcms) usage in omics, especially for untergeted discovery to biojulia
cossio
@cossio
Is it possible to bridge these BioJulia rooms into the Julia slack?
Guillermo Luque
@gluque
Hi there. Is it possible to open a gzipped FASTA using FASTX? I have tried with GzipDecompressorStream from CodecZlib, but not sure how to make the stream readable by FASTA.Reader()
Ciarán O'Mara
@CiaranOMara
@gluque, that seems to be fixed in an unrelease commit.
You can get around this issue by setting up the reader in the following way,
io = open("data/genomic-seq.fasta.gz")
stream = GzipDecompressorStream(io)
reader = FASTA.Reader(FASTA.State(stream, 1, 1, false), nothing)
Guillermo Luque
@gluque
Thanks @CiaranOMara, it works like a charm.
cossio
@cossio
Why should I add the BioJulia registry?
cossio
@cossio
Seems like I can install packages like BioSequences without adding this registry
kdyrhage
@kdyrhage
@cossio You're probably getting v1.1.0, not the latest which is v2.0.1
cossio
@cossio
Any suggestions to deal with taxonomy data in Julia?
Mateusz Kaduk
@mateusz-kaduk_gitlab
Can we read CRAM files with BioJulia?
ksun
@KellySYM
I'm trying to install packages like BioSequences after adding the BioJulia registry, but got the following error message:ERROR: cannot find name corresponding to UUID 861a8166-3701-5b0c-9a16-15d98fcdc6aa in a registry
any ideas how I can fix this? thanks!
Rudy Pelicaen
@rpelicae_gitlab
I have exactly the same problem as ksun! Any solution for this?
Rudy Pelicaen
@rpelicae_gitlab
I found that the UUID 861a8166-3701-5b0c-9a16-15d98fcdc6aa corresponds to an identifier 'Combinatorics' in the Compat.toml file of the BioSequences folder in the BioJulia Registry. Maybe this can help to solve the problem? Thanks.
Ben J. Ward
@BenJWard
Are you able to install combinatorics with your julia setup using pkg add Combinatorics?
Is is also present and correct in the General registry: https://github.com/JuliaRegistries/General/blob/master/C/Combinatorics/Package.toml
Ben J. Ward
@BenJWard
I would make sure you have both the general registry and the biojulia registry installed and up to date..
using Pkg.Registry
Registry.add(Registry.RegistrySpec(url = "https://github.com/JuliaRegistries/General.git"))
Registry.add(Registry.RegistrySpec(url = "https://github.com/BioJulia/BioJuliaRegistry.git"))
ksun
@KellySYM
I could install BioSequences prior to adding the BioJulia registry, but not after adding it.
Rudy Pelicaen
@rpelicae_gitlab
Ok I could install BioSequences after adding the general Julia registry. Thanks for the help. It could be useful to specify this on the BioJulia page for Julia newcomers (like me). Excited to explore BioJulia!
Matt Karikomi
@mkarikom
any advice on which package to map systematic gene names (like "SAMD11") to database indices (like "ENSG00000187634")?
looks like BioServices.jl is the one, maybe...
Mateusz Kaduk
@matkad_gitlab
Hi, can I use use pairalign such that gaps in the target (database) are not allowed? or change the cost model just for database sequence?
or better have a different higher penalty cost for the target database sequence
Mateusz Kaduk
@matkad_gitlab
For example https://biopython.org/DIST/docs/api/Bio.Align.PairwiseAligner-class.html allows target or query specific penalties
Mateusz Kaduk
@mateusz-kaduk_gitlab
solved, nvm :)
Dan Kool
@kool7d
hi, everyone! I'm working on a Bio visualization package called BioMakie.jl
I would like to make it part of BioJulia
Some of the basic functionality is there, but there is a lot more coming. I think I need a little help getting it off the ground. For example, I can't get the docs to deploy
Pavel V. Dimens
@pdimens
@kool7d whats the specific error preventing deployment? I don't have experience specific to Documentor.jl, but Ive dealt with GitHubActions deployment token issues with VuePress, Docusaurus, and Franklin and maybe it's the same issue.
Dan Kool
@kool7d
right now it is a dependency problem I think, making Travis unhappy, but we will see
it's running its tests
Joe Greener
@jgreener64
From a quick look your Travis script seems okay, though Documenter has changed it's Travis docs since I last used it.
Maybe update to latest Julia?
Aadam
@aadimator
Can anyone help me with this, or guide me in the right direction to tackle this problem? BioJulia/BioAlignments.jl#43