# Renaming IDs in a GFF3 **URL:** \ **Category:** Biology, Health, and Medicine\ **Created:** [January 23, 2020, 8:15am UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687 "2020-01-23T08:15:13Z")\ **Posts on this page:** 20\ **Page:** 1

**Author:** ![mictadlo](https://avatars.discourse-cdn.com/v4/letter/m/5daacb/32.png) [@mictadlo](https://discourse.julialang.org/u/mictadlo)\ **Post date:** [January 23, 2020, 8:15am UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/1 "2020-01-23T08:15:13Z")

Hi, are there any examples of renaming IDs in a GFF3 file? Thank you in advance, ---

**Author:** ![kdyrhage](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kdyrhage/32/2326_2.png) [@kdyrhage](https://discourse.julialang.org/u/kdyrhage)\ **Post date:** [January 23, 2020, 10:36am UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/2 "2020-01-23T10:36:21Z")

If you can convert it to GenBank format you can do it easily with [GenomicAnnotations.jl](https://github.com/kdyrhage/GenomicAnnotations.jl). Adding GFF support is on my todo-list, but as I have no use for it myself it has low priority. ---

**Author:** ![kevbonham](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kevbonham/32/216165_2.png) [@kevbonham](https://discourse.julialang.org/u/kevbonham)\ **Post date:** [January 23, 2020, 1:49pm UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/3 "2020-01-23T13:49:13Z")

Woah, when did a gbk parser get added? I’ve been meaning to do this for like 3 years 😆. Is it written in julia or wrapping something else? ---

**Author:** ![kdyrhage](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kdyrhage/32/2326_2.png) [@kdyrhage](https://discourse.julialang.org/u/kdyrhage)\ **Post date:** [January 23, 2020, 2:25pm UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/4 "2020-01-23T14:25:19Z")

It’s pure Julia. I think I wrote the first version almost three years ago now! It’s only been public for about a year I think, though. I guess I haven’t advertised\* it very well. The next version will be in BioJuliaRegistry instead of General, which should make it easier to find. (\*speaking of which, the whole reason I started GenomicAnnotations.jl was to make [GenomicMaps.jl](https://github.com/kdyrhage/GenomicMaps.jl)) I wrote a quick parser for GFF files (which, surprise surprise, was much easier than for GenBank files), and it seems to work just fine. Unless I run into any problems I’ll add a way to write to GFF and upload it. ---

**Author:** ![kevbonham](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kevbonham/32/216165_2.png) [@kevbonham](https://discourse.julialang.org/u/kevbonham)\ **Post date:** [January 23, 2020, 2:29pm UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/5 "2020-01-23T14:29:37Z")

Neat! I see you didn’t use the FSM approach that other BioJulia parsers use. That probably makes sense, (that’s what I tinkered with and it was rough), but have you benchmarked it against some other language parsers? There’s a guy on a forum I’m part of that always brings up the need for a genbank parser before he’ll even consider trying a language out - he suggested testing against the suite that BioPython uses. Let me know if you’re interested in a PR to add those tests, I’d love to be able to go to him with this in hand 🙂 ---

**Author:** ![kdyrhage](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kdyrhage/32/2326_2.png) [@kdyrhage](https://discourse.julialang.org/u/kdyrhage)\ **Post date:** [January 23, 2020, 2:37pm UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/6 "2020-01-23T14:37:21Z")

I haven’t compared it to other parsers. I try to optimise things when I notice that something is performing poorly, but I only work with bacterial genomes so my needs aren’t that great. I tried rewriting the parser using Automa.jl at some point, but once it got too complex it just wouldn’t compile anymore so I gave up on that idea. Absolutely, any form of contribution is welcome! ---

**Author:** ![kdyrhage](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kdyrhage/32/2326_2.png) [@kdyrhage](https://discourse.julialang.org/u/kdyrhage)\ **Post date:** [January 23, 2020, 3:55pm UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/7 "2020-01-23T15:55:48Z")

I have now added a GFF parser. It worked for the file I tested it on, at least. Currently it’s on the branch “parsegff”, so you can install it with: ```julia (v1.3) pkg> add GenomicAnnotations#parsegff ``` Use `readgff(filepath)` to read the file, and `printgff(filepath, annotations)` to write them to a file after modifying the IDs. The documentation for GenomicAnnotations explains how to modify the data. ---

**Author:** ![mictadlo](https://avatars.discourse-cdn.com/v4/letter/m/5daacb/32.png) [@mictadlo](https://discourse.julialang.org/u/mictadlo)\ **Post date:** [January 24, 2020, 3:24am UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/8 "2020-01-24T03:24:09Z")

Thank you for such a quick implementation. Unfortunately, I ran into this problem: ```julia julia> using GenomicAnnotations julia> chr=readgff("/Users/lorencm/projects/bioinf-scripts/data/NbV1Ch08-augustus.hints_utr.gff3") ERROR: BoundsError: attempt to access 1-element Array{SubString{String},1} at index [2] Stacktrace: [1] indexed_iterate at ./array.jl:744 [inlined] [2] parsechromosome_gff(::Array{String,1}, ::Type) at /Users/lorencm/.julia/packages/GenomicAnnotations/Y7qTk/src/readgbk.jl:261 [3] #readgff#33(::Bool, ::typeof(readgff), ::IOStream, ::Type) at /Users/lorencm/.julia/packages/GenomicAnnotations/Y7qTk/src/readgbk.jl:316 [4] readgff at /Users/lorencm/.julia/packages/GenomicAnnotations/Y7qTk/src/readgbk.jl:300 [inlined] [5] #30 at /Users/lorencm/.julia/packages/GenomicAnnotations/Y7qTk/src/readgbk.jl:295 [inlined] [6] #open#271(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(open), ::GenomicAnnotations.var"#30#32"{DataType}, ::String) at ./io.jl:298 [7] open(::Function, ::String) at ./io.jl:296 [8] #readgff#28(::Bool, ::typeof(readgff), ::String, ::Type) at /Users/lorencm/.julia/packages/GenomicAnnotations/Y7qTk/src/readgbk.jl:295 [9] readgff at /Users/lorencm/.julia/packages/GenomicAnnotations/Y7qTk/src/readgbk.jl:291 [inlined] (repeats 2 times) [10] top-level scope at none:0 ``` I used Braker2’s GFF3 file: ```julia NbV1Ch08 AUGUSTUS gene 7015 29794 0.01 - . ID=g1; NbV1Ch08 AUGUSTUS mRNA 7015 29794 0.01 - . ID=g1.t1;Parent=g1 NbV1Ch08 AUGUSTUS transcription_end_site 7015 7015 . - . Parent=g1.t1; NbV1Ch08 AUGUSTUS three_prime_utr 7015 8531 0.2 - . ID=g1.t1.3UTR1;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 7015 8747 . - . ID=g1.t1.exon1;Parent=g1.t1; NbV1Ch08 AUGUSTUS stop_codon 8532 8534 . - 0 Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 8532 8747 0.31 - 0 ID=g1.t1.CDS1;Parent=g1.t1 NbV1Ch08 AUGUSTUS intron 8748 9191 0.49 - . Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 9192 9342 0.66 - 1 ID=g1.t1.CDS2;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 9192 9342 . - . ID=g1.t1.exon2;Parent=g1.t1; bash-3.2$ head -n 100 /Users/lorencm/projects/bioinf-scripts/data/NbV1Ch08-augustus.hints_utr.gff3 NbV1Ch08 AUGUSTUS gene 7015 29794 0.01 - . ID=g1; NbV1Ch08 AUGUSTUS mRNA 7015 29794 0.01 - . ID=g1.t1;Parent=g1 NbV1Ch08 AUGUSTUS transcription_end_site 7015 7015 . - . Parent=g1.t1; NbV1Ch08 AUGUSTUS three_prime_utr 7015 8531 0.2 - . ID=g1.t1.3UTR1;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 7015 8747 . - . ID=g1.t1.exon1;Parent=g1.t1; NbV1Ch08 AUGUSTUS stop_codon 8532 8534 . - 0 Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 8532 8747 0.31 - 0 ID=g1.t1.CDS1;Parent=g1.t1 NbV1Ch08 AUGUSTUS intron 8748 9191 0.49 - . Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 9192 9342 0.66 - 1 ID=g1.t1.CDS2;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 9192 9342 . - . ID=g1.t1.exon2;Parent=g1.t1; NbV1Ch08 AUGUSTUS intron 9343 9915 0.58 - . Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 9916 10006 0.71 - 2 ID=g1.t1.CDS3;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 9916 10006 . - . ID=g1.t1.exon3;Parent=g1.t1; NbV1Ch08 AUGUSTUS intron 10007 10101 0.74 - . Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 10102 10201 0.78 - 0 ID=g1.t1.CDS4;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 10102 10201 . - . ID=g1.t1.exon4;Parent=g1.t1; NbV1Ch08 AUGUSTUS intron 10202 10712 0.8 - . Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 10713 11107 0.11 - 2 ID=g1.t1.CDS5;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 10713 11107 . - . ID=g1.t1.exon5;Parent=g1.t1; NbV1Ch08 AUGUSTUS intron 11108 11569 0.07 - . Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 11570 12151 0.09 - 2 ID=g1.t1.CDS6;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 11570 12151 . - . ID=g1.t1.exon6;Parent=g1.t1; NbV1Ch08 AUGUSTUS intron 12152 12588 0.34 - . Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 12589 12717 0.39 - 2 ID=g1.t1.CDS7;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 12589 12717 . - . ID=g1.t1.exon7;Parent=g1.t1; NbV1Ch08 AUGUSTUS intron 12718 12789 0.42 - . Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 12790 13075 0.39 - 0 ID=g1.t1.CDS8;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 12790 13075 . - . ID=g1.t1.exon8;Parent=g1.t1; NbV1Ch08 AUGUSTUS intron 13076 14832 0.51 - . Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 14833 15009 0.39 - 0 ID=g1.t1.CDS9;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 14833 15009 . - . ID=g1.t1.exon9;Parent=g1.t1; NbV1Ch08 AUGUSTUS intron 15010 15278 0.59 - . Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 15279 15415 0.56 - 2 ID=g1.t1.CDS10;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 15279 15415 . - . ID=g1.t1.exon10;Parent=g1.t1; NbV1Ch08 AUGUSTUS intron 15416 15487 0.58 - . Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 15488 15612 0.96 - 1 ID=g1.t1.CDS11;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 15488 15612 . - . ID=g1.t1.exon11;Parent=g1.t1; NbV1Ch08 AUGUSTUS intron 15613 15706 0.96 - . Parent=g1.t1; NbV1Ch08 AUGUSTUS CDS 15707 15957 0.98 - 0 ID=g1.t1.CDS12;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 15707 15958 . - . ID=g1.t1.exon12;Parent=g1.t1; NbV1Ch08 AUGUSTUS start_codon 15955 15957 . - 0 Parent=g1.t1; NbV1Ch08 AUGUSTUS five_prime_utr 15958 15958 0.99 - . ID=g1.t1.5UTR1;Parent=g1.t1 NbV1Ch08 AUGUSTUS five_prime_utr 27458 28250 0.37 - . ID=g1.t1.5UTR2;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 27458 28250 . - . ID=g1.t1.exon13;Parent=g1.t1; NbV1Ch08 AUGUSTUS five_prime_utr 29272 29794 0.08 - . ID=g1.t1.5UTR3;Parent=g1.t1 NbV1Ch08 AUGUSTUS exon 29272 29794 . - . ID=g1.t1.exon14;Parent=g1.t1; NbV1Ch08 AUGUSTUS transcription_start_site 29794 29794 . - . Parent=g1.t1; ``` What did I miss? Thank you in advance, ---

**Author:** ![mictadlo](https://avatars.discourse-cdn.com/v4/letter/m/5daacb/32.png) [@mictadlo](https://discourse.julialang.org/u/mictadlo)\ **Post date:** [January 24, 2020, 3:26am UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/9 "2020-01-24T03:26:28Z")

**Author:** ![kdyrhage](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kdyrhage/32/2326_2.png) [@kdyrhage](https://discourse.julialang.org/u/kdyrhage)\ **Post date:** [January 24, 2020, 8:28am UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/10 "2020-01-24T08:28:47Z")

I don’t know whether it’s against the [GFF3 specifications](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) or not, but the problem stems from the trailing semicolons. Either way I added a fix. After updating, you should be able to change the IDs with something like: ```julia using GenomicAnnotations chrs = readgff(filepath) for (i, gene) in enumerate(@genes(chrs, !ismissing(:ID))) gene.ID = "newid_$(string(i, pad=4))" end printgff(newfilepath, chrs) ``` It’s not important for the parser, but the file is supposed to have a header specifying the GFF version, so it is not following the specifications. ---

**Author:** ![mictadlo](https://avatars.discourse-cdn.com/v4/letter/m/5daacb/32.png) [@mictadlo](https://discourse.julialang.org/u/mictadlo)\ **Post date:** [January 24, 2020, 8:48am UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/11 "2020-01-24T08:48:36Z")

Thank you, but while updating I got an error: > (v1.3) pkg\> update GenomicAnnotations#parsegff > ERROR: invalid token What did I miss? Thank you in advance, ---

**Author:** ![kdyrhage](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kdyrhage/32/2326_2.png) [@kdyrhage](https://discourse.julialang.org/u/kdyrhage)\ **Post date:** [January 24, 2020, 8:52am UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/12 "2020-01-24T08:52:26Z")

I think just ```julia (v1.3) pkg> up ``` should work. If not, try: ```julia (v1.3) pkg> rm GenomicAnnotations (v1.3) pkg> add GenomicAnnotations#parsegff ``` ---

**Author:** ![mictadlo](https://avatars.discourse-cdn.com/v4/letter/m/5daacb/32.png) [@mictadlo](https://discourse.julialang.org/u/mictadlo)\ **Post date:** [January 24, 2020, 9:27am UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/13 "2020-01-24T09:27:07Z")

Thank `up` worked but now I got a new error: > julia\> using GenomicAnnotations > [Info: Precompiling GenomicAnnotations [4f8a0a0a-376d-5ac0-ab14-e88793df67f0] > > julia\> chr=readgff(“/Users/lorencm/projects/bioinf-scripts/data/NbV1Ch08-augustus.hints\_utr.gff3”) > 1-element Array{Chromosome{Gene},1}: > Chromosome ‘NbV1Ch08’ (0 bp) with 136090 annotations > > julia\> print(chr) > Chromosome{Gene}[Chromosome ‘NbV1Ch08’ (0 bp) with 136090 annotations > ] > julia\> for gene in chr.genes > print(gene) > end > ERROR: type Array has no field genes > Stacktrace: > [1] getproperty(::Array{Chromosome{Gene},1}, ::Symbol) at ./Base.jl:20 > [2] top-level scope at ./REPL[13]:1 What did I miss? ---

**Author:** ![kdyrhage](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kdyrhage/32/2326_2.png) [@kdyrhage](https://discourse.julialang.org/u/kdyrhage)\ **Post date:** [January 24, 2020, 9:45am UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/14 "2020-01-24T09:45:23Z")

GBK/GFF files can contain multiple chromosomes, so `readgff` returns an array. There are multiple ways you can deal with this, so pick the one that suits you best. You can: 1. use the macro `@genes(chrs)` to iterate over the genes from all chromosomes: ```julia for gene in @genes(chrs) ... end ``` 1. iterate over the chromosomes separately: ```julia for chr in chrs for gene in chr.genes ... end end ``` 1. store only one chromosome in `chr`: ```julia chr = readgff(filepath)[1] for gene in chr.genes .... end ``` I recommend option 1, and if your file only contains one chromosome option 3 (`@genes` works on individual `Chromosome`s or arrays of `Chromosome`s, so you can combine the two). ---

**Author:** ![mictadlo](https://avatars.discourse-cdn.com/v4/letter/m/5daacb/32.png) [@mictadlo](https://discourse.julialang.org/u/mictadlo)\ **Post date:** [January 24, 2020, 10:46am UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/15 "2020-01-24T10:46:40Z")

Thank you. I used the following code but I get unexpected output: > NbV1Ch08\_missing > NbV1Ch08\_missing > NbV1Ch08\_missing > NbV1Ch08\_missing > NbV1Ch08\_missing > NbV1Ch08\_missing with the below code: ```julia using GenomicAnnotations chrs=readgff("/Users/lorencm/projects/bioinf-scripts/data/NbV1Ch08-augustus.hints_utr.gff3") for chr in chrs for gene in chr.genes println("$(chr.name)_$(gene.id)") end end ``` How can I access the gene’s ids? Thank you in advance, ---

**Author:** ![kdyrhage](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kdyrhage/32/2326_2.png) [@kdyrhage](https://discourse.julialang.org/u/kdyrhage)\ **Post date:** [January 24, 2020, 10:55am UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/16 "2020-01-24T10:55:38Z")

Attribute names are case-sensitive, so use `gene.ID`, not `gene.id`. Judging by the partial file you posted, not all entries have an ID, so I recommend using the version with `@genes` that I posted earlier: ```julia for gene in @genes(chr, !ismissing(:ID)) println("$(chr.name)_$(gene.ID)") end ``` This will iterate over the entries that _do_ have and ID. Otherwise, for entries that lack an ID `gene.ID` will, again, return `missing`. ---

**Author:** ![mictadlo](https://avatars.discourse-cdn.com/v4/letter/m/5daacb/32.png) [@mictadlo](https://discourse.julialang.org/u/mictadlo)\ **Post date:** [January 24, 2020, 12:09pm UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/17 "2020-01-24T12:09:49Z")

Thank you but I ran into a new error: ```julia julia> chr=readgff("/Users/lorencm/projects/bioinf-scripts/data/NbV1Ch08-augustus.hints_utr.gff3") 1-element Array{Chromosome{Gene},1}: Chromosome 'NbV1Ch08' (0 bp) with 136090 annotations julia> for gene in @genes(chr, !ismissing(:ID)) println("$(chr.name)_$(gene.ID)") end ERROR: type Array has no field name Stacktrace: [1] getproperty(::Array{Chromosome{Gene},1}, ::Symbol) at ./Base.jl:20 [2] top-level scope at /Users/lorencm/.julia/packages/GenomicAnnotations/4kJOh/src/macro.jl:2 ``` Please find [here](https://drive.google.com/open?id=1mM-LNCDHV3YWZ4rC486o_gf6cUpjNXTh) a GFF3 for one chromosome. Thank you in advance ---

**Author:** ![kdyrhage](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kdyrhage/32/2326_2.png) [@kdyrhage](https://discourse.julialang.org/u/kdyrhage)\ **Post date:** [January 24, 2020, 12:22pm UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/18 "2020-01-24T12:22:18Z")

Your `chr` is still an `Array{Chromosome}`. In this case there is only one chromosome, so you can access the name with `chr[1].name`. For a more general solution, use `parent(gene).name`. `parent(gene::Gene)` returns the `Chromosome` that contains `gene`. The following example will work for a GFF file with any number of chromosomes: ```julia using GenomicAnnotations chrs = readgff("/Users/lorencm/projects/bioinf-scripts/data/NbV1Ch08-augustus.hints_utr.gff3") for gene in @genes(chrs, !ismissing(:ID)) println("$(parent(gene).name)_$(gene.ID)") end ``` ---

**Author:** ![mictadlo](https://avatars.discourse-cdn.com/v4/letter/m/5daacb/32.png) [@mictadlo](https://discourse.julialang.org/u/mictadlo)\ **Post date:** [January 24, 2020, 1:23pm UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/19 "2020-01-24T13:23:05Z")

Thank you. I added a counter which lead that each feature gets a new ID rather each gene. ```julia NbV1Ch08_g5742.t1_078390 NbV1Ch08_g5742.t1.3UTR1_078391 NbV1Ch08_g5742.t1.exon1_078392 NbV1Ch08_g5742.t1.CDS1_078393 NbV1Ch08_g5742.t1.CDS2_078394 NbV1Ch08_g5742.t1.exon2_078395 NbV1Ch08_g5742.t1.CDS3_078396 NbV1Ch08_g5742.t1.exon3_078397 NbV1Ch08_g5742.t1.CDS4_078398 NbV1Ch08_g5742.t1.exon4_078399 NbV1Ch08_g5742.t1.CDS5_078400 NbV1Ch08_g5742.t1.exon5_078401 NbV1Ch08_g5742.t1.CDS6_078402 NbV1Ch08_g5742.t1.exon6_078403 NbV1Ch08_g5742.t1.CDS7_078404 NbV1Ch08_g5742.t1.exon7_078405 NbV1Ch08_g5742.t1.CDS8_078406 NbV1Ch08_g5742.t1.exon8_078407 NbV1Ch08_g5742.t1.CDS9_078408 NbV1Ch08_g5742.t1.exon9_078409 NbV1Ch08_g5742.t1.CDS10_078410 NbV1Ch08_g5742.t1.exon10_078411 NbV1Ch08_g5742.t1.CDS11_078412 NbV1Ch08_g5742.t1.exon11_078413 NbV1Ch08_g5742.t1.CDS12_078414 NbV1Ch08_g5742.t1.exon12_078415 NbV1Ch08_g5742.t1.CDS13_078416 NbV1Ch08_g5742.t1.exon13_078417 NbV1Ch08_g5742.t1.CDS14_078418 NbV1Ch08_g5742.t1.exon14_078419 NbV1Ch08_g5742.t1.CDS15_078420 NbV1Ch08_g5742.t1.exon15_078421 NbV1Ch08_g5742.t1.5UTR1_078422 NbV1Ch08_g5742.t2_078423 NbV1Ch08_g5742.t2.3UTR1_078424 NbV1Ch08_g5742.t2.exon1_078425 NbV1Ch08_g5742.t2.CDS1_078426 NbV1Ch08_g5742.t2.CDS2_078427 NbV1Ch08_g5742.t2.exon2_078428 NbV1Ch08_g5742.t2.CDS3_078429 NbV1Ch08_g5742.t2.exon3_078430 NbV1Ch08_g5742.t2.CDS4_078431 NbV1Ch08_g5742.t2.exon4_078432 NbV1Ch08_g5742.t2.CDS5_078433 NbV1Ch08_g5742.t2.exon5_078434 NbV1Ch08_g5742.t2.CDS6_078435 NbV1Ch08_g5742.t2.exon6_078436 NbV1Ch08_g5742.t2.5UTR1_078437 ``` I would have expected to see: ```julia NbV1Ch08_g5742.t1_078390 NbV1Ch08_g5742.t1.3UTR1_078390 NbV1Ch08_g5742.t1.exon1_078390 NbV1Ch08_g5742.t1.CDS1_078390 ... ``` Here is the update code: ```julia using GenomicAnnotations chrs = readgff("/Users/lorencm/projects/bioinf-scripts/data/NbV1Ch08-augustus.hints_utr.gff3") for (count, gene) in enumerate(@genes(chrs, !ismissing(:ID))) newID = lpad(count, 6, '0') println("$(parent(gene).name)_$(gene.ID)_$(newID)") end ``` Is there a better way to implement a counter? Thank you in advance, ---

**Author:** ![kdyrhage](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kdyrhage/32/2326_2.png) [@kdyrhage](https://discourse.julialang.org/u/kdyrhage)\ **Post date:** [January 24, 2020, 1:32pm UTC](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687/20 "2020-01-24T13:32:32Z")

Something like this? ```julia using GenomicAnnotations chrs = readgff("/Users/lorencm/projects/bioinf-scripts/data/NbV1Ch08-augustus.hints_utr.gff3") currentID = 0 for gene in @genes(chrs, !ismissing(:ID)) if feature(gene) == :gene global currentID += 1 end newID = lpad(currentID, 6, '0') println("$(parent(gene).name)_$(gene.ID)_$newID") end ``` [Next page](https://discourse.julialang.org/t/renaming-ids-in-a-gff3/33687.md?page=2)