product info not printout in tbl

[shuhailaMSR]

hi, I am using this convert_gff3_to_ncbi_tbl.py to convert gff3 into tbl and it work but there are problem that it does not print out protein_id and product in tbl.

INPUT ##gff-version 3 JA01000001 AUG gene 91 2658 . - . ID=g1;locus_tag=K_g1 JA01000001 AUG mRNA 91 2658 . - . ID=g1.t1;Parent=g1;locus_tag=K_g1;protein_id=K_g1;product=Transcription factor JA01000001 AUG CDS 94 2658 . - 0 ID=g1.t1.cds;Parent=g1.t1;locus_tag=K_g1 JA01000001 AUG exon 94 2658 . - . ID=g1.t1.exon1;Parent=g1.t1;locus_tag=K_g1

EXPECTED

Feature gnl|WGS:JA|SeqID|gb|JA01000001 2658 91 gene locus_tag K_g1 2658 94 mRNA protein_id K_g1 product Transcription factor 2658 94 CDS

but the OUTPUT

Feature gnl|WGS:JA|SeqID|gb|JA01000001 2658 91 gene locus_tag K_g1 2658 94 mRNA 2658 94 CDS

[jorvis]

Interesting. This section of code first checks to see if the gff3 has a polypeptide line and uses the annotation there, else falls back to the RNA feature, which yours has.

https://github.com/jorvis/biocode/blob/master/lib/biocode/tbl.py#L147

Are you comfortable posting your (compressed) GFF3 to this issue?

[shuhailaMSR]

do you mean gff3 file? k_gff3.txt