EOFError: read end of file

[junjunlab]

EOFError: read end of file

Hello, I use while loop to read GFF3 file but I got this error.I do not know how it happens and how to solve it. Here is my code:

# Import the GFF3 module.
using GFF3

exonDict = Dict{String,Int64}()

# Open a GFF3 file.
reader = open(GFF3.Reader, "Homo_sapiens.GRCh38.106.gff3")

# Pre-allocate record.
record = GFF3.Record()

# Iterate over records.
while !eof(reader)
    empty!(record)
    read!(reader,record)
    # do something
    if GFF3.featuretype(record) == "exon"
        transid = split(GFF3.attributes(record,"Parent")[1],":")[2]
        exonLength = abs(GFF3.seqend(record) - GFF3.seqstart(record)) + 1
        # println(exonLength)
        if !haskey(exonDict,transid)
            exonDict[transid] = exonLength
        else
            exonDict[transid] += exonLength
        end
    end
end

# Finally, close the reader.
close(reader)

Thank you for your reply!

[CiaranOMara]

Your code is reasonable and should work.

In the middle time, you could adjust your loop to use the following, which works because the iterator for the reader catches the EOF error.

for record in reader
    # do something
    if GFF3.featuretype(record) == "exon"
        transid = split(GFF3.attributes(record,"Parent")[1],":")[2]
        exonLength = abs(GFF3.seqend(record) - GFF3.seqstart(record)) + 1
        # println(exonLength)
        if !haskey(exonDict,transid)
            exonDict[transid] = exonLength
        else
            exonDict[transid] += exonLength
        end
    end
end