# BigWig Reader

**URL:** <https://discourse.julialang.org/t/bigwig-reader/4677>\
**Category:** Biology, Health, and Medicine\
**Tags:** question\
**Created:** [July 6, 2017, 3:27am UTC](https://discourse.julialang.org/t/bigwig-reader/4677 "2017-07-06T03:27:02Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![PoisonAlien](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/poisonalien/32/1310_2.png) [@PoisonAlien](https://discourse.julialang.org/u/PoisonAlien)\
**Post date:** [July 6, 2017, 3:27am UTC](https://discourse.julialang.org/t/bigwig-reader/4677/1 "2017-07-06T03:27:02Z")

</div>

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:

```julia
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

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<div class="post-metadata">

**Author:** ![bicycle1885](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/bicycle1885/32/107_2.png) [@bicycle1885](https://discourse.julialang.org/u/bicycle1885)\
**Post date:** [July 6, 2017, 4:42am UTC](https://discourse.julialang.org/t/bigwig-reader/4677/2 "2017-07-06T04:42:18Z")

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Do you use Bio.jl or [GenomicFeatures.jl](https://github.com/BioJulia/GenomicFeatures.jl)?

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

```julia
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.

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<div class="post-metadata">

**Author:** ![PoisonAlien](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/poisonalien/32/1310_2.png) [@PoisonAlien](https://discourse.julialang.org/u/PoisonAlien)\
**Post date:** [July 6, 2017, 5:10am UTC](https://discourse.julialang.org/t/bigwig-reader/4677/3 "2017-07-06T05:10:58Z")

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

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<div class="post-metadata">

**Author:** ![PoisonAlien](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/poisonalien/32/1310_2.png) [@PoisonAlien](https://discourse.julialang.org/u/PoisonAlien)\
**Post date:** [July 6, 2017, 10:25am UTC](https://discourse.julialang.org/t/bigwig-reader/4677/4 "2017-07-06T10:25:11Z")

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

```julia
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 ?

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<div class="post-metadata">

**Author:** ![bicycle1885](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/bicycle1885/32/107_2.png) [@bicycle1885](https://discourse.julialang.org/u/bicycle1885)\
**Post date:** [July 6, 2017, 11:56am UTC](https://discourse.julialang.org/t/bigwig-reader/4677/5 "2017-07-06T11:56:36Z")

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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](https://travis-ci.org/BioJulia/GenomicFeatures.jl/builds/247624406)), which installs GenomicFeatures.jl in a fresh environment. Anyway, I don’t think this is directly related to the package itself.

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<div class="post-metadata">

**Author:** ![PoisonAlien](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/poisonalien/32/1310_2.png) [@PoisonAlien](https://discourse.julialang.org/u/PoisonAlien)\
**Post date:** [July 7, 2017, 3:00am UTC](https://discourse.julialang.org/t/bigwig-reader/4677/6 "2017-07-07T03:00:29Z")

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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.