BigWig Reader

Specific Domains Biology, Health, and Medicine
1

Hi,

Before julia 0.6, I would read BigWig files without any problem

BigWig.Reader(open("foo.bw"))

but after the update, BigWig.Reader seems to be missing. This is the error I am getting:

ERROR: LoadError: type DataType has no field Reader
Stacktrace:
 [1] macro expansion at /home/usr/NGS/julia_scripts/extractBigWigSignal.jl:60 [inlined]
 [2] anonymous at ./<missing>:?
 [3] include_from_node1(::String) at ./loading.jl:569
 [4] include(::String) at ./sysimg.jl:14
 [5] process_options(::Base.JLOptions) at ./client.jl:305
 [6] _start() at ./client.jl:371

BioJulia version: 0.4.7

2

Do you use Bio.jl or GenomicFeatures.jl?

Bio.jl is still under a large reconstruction and does not support Julia 0.6, but GenomicFeatures.jl already support it.

julia> using GenomicFeatures

julia> reader = open(BigWig.Reader, "test/BioFmtSpecimens/BBI/bigWig1.bw");

julia> collect(reader)
2-element Array{GenomicFeatures.BigWig.Record,1}:
 chr1:2-1000  54.0
 chr1:1001-1099  53.0

So, GenomicFeatures.jl is a recommended package now. In the near future, Bio.jl will be build on top of modular packages including GenomicFeatures.jl.

3

Thank you for clarification! I wasn’t aware of GenomicFeatures. I will try it.

4

Hi, I am trying to install GenomicFeatures but I am getting this error.

ERROR: resolve is unable to satisfy package requirements.
  The problem was detected when trying to find a feasible version
  for package BioSequences.
  However, this only means that package BioSequences is involved in an
  unsatisfiable or difficult dependency relation, and the root of
  the problem may be elsewhere.

I tried installing and building BioSequeces manually, but didnt help. Any suggestion ?

5

Hmm, I have no idea. I guess clean install of packages (i.e. removing all packages under ~/.julia and installing GenomicFeatures.jl) will solve the problem because TravisCI passes both on Linux and MacOS (Travis CI - Test and Deploy Your Code with Confidence), which installs GenomicFeatures.jl in a fresh environment. Anyway, I don’t think this is directly related to the package itself.

6

Yes you are correct its not a problem with the package itself. Apologies. Anyways, thanks again. I removed all packages under julia/v0.6 and GenomicFeatures installed smoothly.