gtf_to_tsv.jl

path_gtf = "merged.asm/merged.gtf"
path_ofile = "merged.asm/merged.gtf.txt"


arr_attr = Array{Any,1}()
d_attr = Dict{Any,Any}()


# Extract all attributes
f = open(path_gtf)
for ln in eachline(f)
	for s in split(split(chomp(ln), "\t")[9], "; ")
		if ! in(split(s, " ")[1], arr_attr)
			push!(arr_attr, split(s, " ")[1])
		end
	end
end
close(f)

for s in arr_attr
	println(s)
	println(typeof(s))
end

# Convert Colmun 9 into columns
fw = open(path_ofile, "w")
write(fw, join(["chr"; "V2"; "V3"; "start"; "end"; "V6"; "strand"; "V8"; arr_attr], "\t") * "\n")


f = open(path_gtf)
for ln in eachline(f)
	empty!(d_attr)
	for s in split(split(chomp(ln), "\t")[9], "; ")
		d_attr[split(s, " ")[1]] = replace(split(s, " ")[2], r"[\";]", s"")

	end
	res = join(split(chomp(ln), "\t")[1:8], "\t")
	for s in arr_attr
		if in(s, keys(d_attr))
			res *= "\t" * d_attr[s]
		else
			res *= "\t" * "."
		end
	end
	write(fw, res * "\n")
end
close(f)

close(fw)