Re: Reading GTF file

[mdhe1248]

Background

I am trying to read/load a GTF file, so that I can compute coverage of my sequencing reads on each gene. However, I obtained errors during reading and couldn't access to my GTF file. How could I open a GTF file?
By the way, my GTF file was downloaded from Gencode and contains mouse genome annotations.

Current Behavior

I tried to read my gtf file, but I got an error message.

using GenomicFeatures
GFF3.Reader( "gencode.vM18.annotation.gtf")

ERROR: MethodError: Cannot `convert` an object of type String to an object of type GenomicFeatures.GFF3.Reader
This may have arisen from a call to the constructor GenomicFeatures.GFF3.Reader(...), since type constructors fall back to convert methods.

I tried open, and this time I didn't get any error message.

reader = open(GFF3.Reader, "gencode.vM18.annotation.gtf")

GenomicFeatures.GFF3.Reader(BioCore.Ragel.State{BufferedStreams.BufferedInputStream{IOStream}}(BufferedStreams.BufferedInputStream{IOStream}(<128.0 KiB buffer, 100% filled, data immobilized>), -27, 6, false), false, Symbol[:feature], false, GenomicFeatures.GFF3.Record[], 0, 5)

Then, I executed IntervalCollection, but obtained an error

features = IntervalCollection(reader)

ERROR: GenomicFeatures.GFF3.Reader file format error on line 6 ~>"; gene_t"
Stacktrace:
 [1] _read!(::GenomicFeatures.GFF3.Reader, ::BioCore.Ragel.State{BufferedStreams.BufferedInputStream{IOStream}}, ::GenomicFeatures.GFF3.Record) at /home/donghoon/.julia/v0.6/BioCore/src/ReaderHelper.jl:164
 [2] read! at /home/donghoon/.julia/v0.6/BioCore/src/ReaderHelper.jl:134 [inlined]
 [3] tryread!(::GenomicFeatures.GFF3.Reader, ::GenomicFeatures.GFF3.Record) at /home/donghoon/.julia/v0.6/BioCore/src/Ragel.jl:241                                     
 [4] start(::GenomicFeatures.GFF3.Reader) at /home/donghoon/.julia/v0.6/BioCore/src/Ragel.jl:258                                                                       
 [5] _collect(::Type{GenomicFeatures.Interval{GenomicFeatures.GFF3.Record}}, ::GenomicFeatures.GFF3.Reader, ::Base.SizeUnknown) at ./array.jl:394                      
 [6] GenomicFeatures.IntervalCollection(::GenomicFeatures.GFF3.Reader) at /home/donghoon/.julia/v0.6/GenomicFeatures/src/gff3/reader.jl:73     

Your Environment

• Package Version used: 0.2.1
• Julia Version used: 0.6.4
• Operating System and version (desktop or mobile): Ubuntu 16.04.5
• Link to your project:

[TransGirlCodes]

Hi @mdhe1248, can you provide us with the file you are trying to read? This is a file format error thrown from the reader. This might mean several things, maybe something is not standard about the formatting of the file, or maybe there is a bug in the reader, or maybe the GFF3 grammer we use to generate the reader is too strict.

[mdhe1248]

Hi @benjward ,

GTF is a bit different from GFF3. That may be the reason why I get such errors above. Gencode combined manual annotations from HAVANA group and automatic annotations from Ensembl. https://en.wikipedia.org/wiki/GENCODE

This is the result from head gencode.vM18.annotation.gtf from the terminal.

$head gencode.vM18.annotation.gtf

##description: evidence-based annotation of the mouse genome (GRCm38), version M18 (Ensembl 93)
##provider: GENCODE
##contact: [email protected]
##format: gtf
##date: 2018-07-02
chr1    HAVANA  gene    3073253 3074322 .       +       .       gene_id "ENSMUSG00000102693.1"; gene_type "TEC"; gene_name "RP23-271O17.1"; level 2; havana_gene "OTTMUSG00000049935.1";
chr1    HAVANA  transcript      3073253 3074322 .       +       .       gene_id "ENSMUSG00000102693.1"; transcript_id "ENSMUST00000193812.1"; gene_type "TEC"; gene_name "RP23-271O17.1"; transcript_type "TEC"; transcript_name "RP23-271O17.1-001"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049935.1"; havana_transcript "OTTMUST00000127109.1";
chr1    HAVANA  exon    3073253 3074322 .       +       .       gene_id "ENSMUSG00000102693.1"; transcript_id "ENSMUST00000193812.1"; gene_type "TEC"; gene_name "RP23-271O17.1"; transcript_type "TEC"; transcript_name "RP23-271O17.1-001"; exon_number 1; exon_id "ENSMUSE00001343744.1"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049935.1"; havana_transcript "OTTMUST00000127109.1";
chr1    ENSEMBL gene    3102016 3102125 .       +       .       gene_id "ENSMUSG00000064842.1"; gene_type "snRNA"; gene_name "Gm26206"; level 3;
chr1    ENSEMBL transcript      3102016 3102125 .       +       .       gene_id "ENSMUSG00000064842.1"; transcript_id "ENSMUST00000082908.1"; gene_type "snRNA"; gene_name "Gm26206"; transcript_type "snRNA"; transcript_name "Gm26206-201"; level 3; transcript_support_level "NA"; tag "basic";

GTF is also widely used and is more close to GFF2. Maybe, it would be okay to make GFF2.Reader or GTF.Reader, or some reader that recognizes different extensions. I ran something on R and it has been several hours. I hope Julia can accelerate analysis process.

I downloaded Comprehensive gene annotation from https://www.gencodegenes.org/mouse_releases/current.html

[TransGirlCodes]

Hi @mdhe1248 I'm surprised that we don't already have a GTF parser!
I shall look at making one today at the JuliaCon hackerthon.

[mdhe1248]

Oh, My PI must be there, probably talking about debugger. :)

Thank you for your help.

[TransGirlCodes]

Is your PI Tim Holy? If you can I'd try to convert GTF to GFF3 if you use it with BioJulia, whilst a proper GFF2 parser is worked out.

[jonathanBieler]

Maybe this could be useful : https://github.com/mmkim1210/GeneticsMakie.jl/blob/master/src/parsegtf.jl