GFF3 Record Encode Error in Attributes like ";product=xxx (a; b) xxx"

[cihga39871]

The code:

using GFF3

r = GFF3.Record("Ga0225945_11\timg_core_v400\tCDS\t350909\t352399\t.\t-\t0\tID=2800905551;locus_tag=Ga0225945_11352;product=respiratory nitrite reductase (cytochrome; ammonia-forming) precursor")

Expected Behavior

Expect product attribute to be ["respiratory nitrite reductase (cytochrome; ammonia-forming) precursor"]

Current Behavior

ERROR: ArgumentError: failed to index Any ~>""
Stacktrace:
 [1] macro expansion
   @ C:\Users\x\.julia\packages\GFF3\RXGVR\src\reader.jl:310 [inlined]
 [2] index!(stream::TranscodingStreams.NoopStream{IOBuffer}, record::GFF3.Record)
   @ GFF3 C:\Users\x\.julia\packages\Automa\1KOLQ\src\Stream.jl:126
 [3] index!
   @ C:\Users\x\.julia\packages\GFF3\RXGVR\src\reader.jl:118 [inlined]
 [4] convert
   @ C:\Users\x\.julia\packages\GFF3\RXGVR\src\record.jl:54 [inlined]
 [5] Record
   @ C:\Users\x\.julia\packages\GFF3\RXGVR\src\record.jl:44 [inlined]
 [6] convert(#unused#::Type{GFF3.Record}, str::String)
   @ GFF3 C:\Users\x\.julia\packages\GFF3\RXGVR\src\record.jl:69
 [7] GFF3.Record(str::String)
   @ GFF3 C:\Users\x\.julia\packages\GFF3\RXGVR\src\record.jl:65
 [8] top-level scope
   @ none:1

Possible Solution / Implementation

Treat ; in (), [] and {} as a non separator.

Your Environment

• Package Version used: [af1dc308] GFF3 v0.2.1
• Julia Version used: 1.6.1
• Operating System and version (desktop or mobile): Windows 11
• Link to your project: NA

(@v1.6) pkg> status
      Status `C:\Users\x\.julia\environments\v1.6\Project.toml`
  [c7e460c6] ArgParse v1.1.4
  [c52e3926] Atom v0.12.34
  [336ed68f] CSV v0.9.1
  [a93c6f00] DataFrames v1.2.2
  [1313f7d8] DataFramesMeta v0.9.1
  [31c24e10] Distributions v0.25.16
  [c2308a5c] FASTX v1.2.0
  [af1dc308] GFF3 v0.2.1
  [eeff360b] JobSchedulers v0.1.2
  [e5e0dc1b] Juno v0.8.4
  [ef544631] Pipelines v0.4.0
  [91a5bcdd] Plots v1.21.3
  [f3b207a7] StatsPlots v0.14.27
  [fdbf4ff8] XLSX v0.7.8
  [ddb6d928] YAML v0.4.7

Thank you.

[CiaranOMara]

This is an interesting issue. I had to check the specification for column 9. The semicolon is a reserved character that delimits the attributes. However, the specification stipulates that URL escaped semicolons may be used as part of an attribute tag or value. The URL encoding for a semicolon is %3B.

A possible solution is to URL encode your tags or values with HTTP.

using GFF3
using HTTP

str = "Ga0225945_11\timg_core_v400\tCDS\t350909\t352399\t.\t-\t0\tID=2800905551;locus_tag=Ga0225945_11352;product="*HTTP.escapeuri("respiratory nitrite reductase (cytochrome; ammonia-forming) precursor")

r = GFF3.Record(str)

When reading data back, HTTP.unescapeuri(str) is available if needed.

[cihga39871]

Thank you, Ciaran. I found the record is not stick to the specification, so it is possible OK to throw an error. Because the data is downloaded from JGI, so I cannot escape it unless I parse it manually.

It would be nice if GFF3.jl can hint the user when the data provided is not valid.