Error when loading genebank file from NCBI

[TorkelE]

Hello, I have downloaded a genebank file from NCBI (https://www.ncbi.nlm.nih.gov/nuccore/NC_022898.1?report=genbank then send to -> file -> GeneBank (full))

I then try to open the file using

gbff = readgbk("sequence.gb")

but get an error:

ERROR: ArgumentError: invalid index: nothing of type Nothing
Stacktrace:
 [1] to_index(i::Nothing)
   @ Base ~/julia-1.3.1/bin/../share/julia/base/indices.jl:273

 [2] to_index(A::Array{SubString{String},1}, i::Nothing)
   @ Base ~/julia-1.3.1/bin/../share/julia/base/indices.jl:250

 [3] to_indices
   @ Base ~/julia-1.3.1/bin/../share/julia/base/indices.jl:301 [inlined]

 [4] to_indices
   @ Base ~/julia-1.3.1/bin/../share/julia/base/indices.jl:298 [inlined]

 [5] getindex
   @ ~/julia-1.3.1/bin/../share/julia/base/abstractarray.jl:981 [inlined]

 [6] parseheader(header::String)
   @ GenomicAnnotations.GenBank ~/.julia/packages/GenomicAnnotations/gigUo/src/GenBank/reader.jl:58

 [7] parsechromosome!(stream::TranscodingStreams.TranscodingStream{TranscodingStreams.Noop,IOStream}, record::GenomicAnnotations.Record{Gene})
   @ GenomicAnnotations.GenBank ~/.julia/packages/GenomicAnnotations/gigUo/src/GenBank/reader.jl:227

 [8] tryread!
   @ GenomicAnnotations.GenBank ~/.julia/packages/GenomicAnnotations/gigUo/src/GenBank/reader.jl:49 [inlined]

 [9] iterate
   @ GenomicAnnotations.GenBank ~/.julia/packages/GenomicAnnotations/gigUo/src/GenBank/reader.jl:42 [inlined]

[10] _collect(cont::UnitRange{Int64}, itr::GenomicAnnotations.GenBank.Reader{TranscodingStreams.TranscodingStream{TranscodingStreams.Noop,IOStream}}, ::Base.HasEltype, isz::Base.SizeUnknown)
   @ Base ~/julia-1.3.1/bin/../share/julia/base/array.jl:572

[11] collect
   @ Base ~/julia-1.3.1/bin/../share/julia/base/array.jl:560 [inlined]

[12] readgbk(input::String)
   @ GenomicAnnotations ~/.julia/packages/GenomicAnnotations/gigUo/src/utils.jl:65

[13] top-level scope
   @ REPL[15]:1

It should get noted that if I download the GeneBank file instead (no "(full)"), then I can load it (but there's not much actual content in it).

[kdyrhage]

Seems like the recent API change introduced this. The problem was an empty line at the end, so until the new version has been registered you can just remove the last line of the file.

[TorkelE]

Just confirming that this worked, thanks.