Correct gtf file format (AGAT toolkit)

Question

[tianshenbio]

I used agat_convert_sp_gff2gtf.pl of AGAT toolkit to convert my gff file to gtf file. In the converted gtf file, the double quotes of 'gene_id' are missing:

Bany_Scaf1  maker   gene    201136  207903  .   +   .   Alias "maker-Bany_Scaf1-snap-gene-2.23"; Dbxref "InterPro:IPR019774" "Pfam:PF00351"; ID Bany_03723; Name Bany_03723; Ontology_term "GO:0016714" "GO:0055114"; gene_id Bany_03723
Bany_Scaf1  maker   transcript  201136  207903  .   +   .   Alias "maker-Bany_Scaf1-snap-gene-2.23-mRNA-1"; Dbxref "InterPro:IPR019774" "Pfam:PF00351"; ID "Bany_03723-RA"; Name "Bany_03723-RA"; Ontology_term "GO:0016714" "GO:0055114"; Parent Bany_03723; _AED "0.06"; _QI "45|1|1|1|1|1|7|425|530"; _eAED "0.06"; gene_id Bany_03723; original_biotype mrna; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   exon    201136  201304  .   +   .   ID "Bany_03723-RA:1"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   exon    202687  202770  .   +   .   ID "Bany_03723-RA:2"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   exon    202886  202921  .   +   .   ID "Bany_03723-RA:3"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   exon    203004  203820  .   +   .   ID "Bany_03723-RA:4"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   exon    206097  206223  .   +   .   ID "Bany_03723-RA:5"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   exon    206649  206878  .   +   .   ID "Bany_03723-RA:6"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   exon    207304  207903  .   +   .   ID "Bany_03723-RA:7"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   CDS 201181  201304  .   +   0   ID "Bany_03723-RA:cds"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   CDS 202687  202770  .   +   2   ID "Bany_03723-RA:cds"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   CDS 202886  202921  .   +   2   ID "Bany_03723-RA:cds"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   CDS 203004  203820  .   +   2   ID "Bany_03723-RA:cds"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   CDS 206097  206223  .   +   1   ID "Bany_03723-RA:cds"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   CDS 206649  206878  .   +   0   ID "Bany_03723-RA:cds"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   CDS 207304  207478  .   +   1   ID "Bany_03723-RA:cds"; Parent "Bany_03723-RA"; gene_id Bany_03723; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   five_prime_utr  201136  201180  .   +   .   ID "Bany_03723-RA:five_prime_utr"; Parent "Bany_03723-RA"; gene_id Bany_03723; original_biotype five_prime_UTR; transcript_id "Bany_03723-RA" 
Bany_Scaf1  maker   three_prime_utr 207479  207903  .   +   .   ID "Bany_03723-RA:three_prime_utr"; Parent "Bany_03723-RA"; gene_id Bany_03723; original_biotype three_prime_UTR; transcript_id "Bany_03723-RA"

my gff (already corrected by AGAT.

Bany_Scaf1  maker   gene    201136  207903  .   +   .   ID=Bany_03723;Alias=maker-Bany_Scaf1-snap-gene-2.23;Dbxref=InterPro:IPR019774,Pfam:PF00351;Name=Bany_03723;Ontology_term=GO:0016714,GO:0055114
Bany_Scaf1  maker   mRNA    201136  207903  .   +   .   ID=Bany_03723-RA;Parent=Bany_03723;Alias=maker-Bany_Scaf1-snap-gene-2.23-mRNA-1;Dbxref=InterPro:IPR019774,Pfam:PF00351;Name=Bany_03723-RA;Ontology_term=GO:0016714,GO:0055114;_AED=0.06;_QI=45|1|1|1|1|1|7|425|530;_eAED=0.06
Bany_Scaf1  maker   exon    201136  201304  .   +   .   ID=Bany_03723-RA:1;Parent=Bany_03723-RA
Bany_Scaf1  maker   exon    202687  202770  .   +   .   ID=Bany_03723-RA:2;Parent=Bany_03723-RA
Bany_Scaf1  maker   exon    202886  202921  .   +   .   ID=Bany_03723-RA:3;Parent=Bany_03723-RA
Bany_Scaf1  maker   exon    203004  203820  .   +   .   ID=Bany_03723-RA:4;Parent=Bany_03723-RA
Bany_Scaf1  maker   exon    206097  206223  .   +   .   ID=Bany_03723-RA:5;Parent=Bany_03723-RA
Bany_Scaf1  maker   exon    206649  206878  .   +   .   ID=Bany_03723-RA:6;Parent=Bany_03723-RA
Bany_Scaf1  maker   exon    207304  207903  .   +   .   ID=Bany_03723-RA:7;Parent=Bany_03723-RA
Bany_Scaf1  maker   CDS 201181  201304  .   +   0   ID=Bany_03723-RA:cds;Parent=Bany_03723-RA
Bany_Scaf1  maker   CDS 202687  202770  .   +   2   ID=Bany_03723-RA:cds;Parent=Bany_03723-RA
Bany_Scaf1  maker   CDS 202886  202921  .   +   2   ID=Bany_03723-RA:cds;Parent=Bany_03723-RA
Bany_Scaf1  maker   CDS 203004  203820  .   +   2   ID=Bany_03723-RA:cds;Parent=Bany_03723-RA
Bany_Scaf1  maker   CDS 206097  206223  .   +   1   ID=Bany_03723-RA:cds;Parent=Bany_03723-RA
Bany_Scaf1  maker   CDS 206649  206878  .   +   0   ID=Bany_03723-RA:cds;Parent=Bany_03723-RA
Bany_Scaf1  maker   CDS 207304  207478  .   +   1   ID=Bany_03723-RA:cds;Parent=Bany_03723-RA
Bany_Scaf1  maker   five_prime_UTR  201136  201180  .   +   .   ID=Bany_03723-RA:five_prime_utr;Parent=Bany_03723-RA
Bany_Scaf1  maker   three_prime_UTR 207479  207903  .   +   .   ID=Bany_03723-RA:three_prime_utr;Parent=Bany_03723-RA

How can I add the missing double quotes?

[alex.zaccaron]

AGAT should produce a correct GTF file. Is there anything wrong with your GFF? A new version of AGAT was released recently and a few issues were fixed. Try to update it.

[tianshenbio]

Added my gff in the post. My gff file was checked and correct by AGAT already, and I am using v0.3.0

Answer 1

[Juke34]

Hi, thank you for pointing it, I had forgot about it! The problem is related to Bioperl see here. I have a patch to fix the problem in Bioperl but I was waiting some feedbacks. I will try to include the necessary changes specifically in the agat_convert_sp_gff2gtf.pl script. It should be fixed in a next release.

[tianshenbio]

Hi, thank you for your updates! I managed to fix it in Linux, hope this can be fixed in the next release.