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fmalmeida / gff-toolbox

Gff-toolbox is a toolbox of commands that enables one to get the gist of their GFF annotation files, as well as to analyse them in different ways.
https://github.com/fmalmeida/gff-toolbox/wiki
GNU General Public License v3.0
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Problem with "gff3_ID_generator.py" #10

Closed MesYosra closed 1 year ago

MesYosra commented 1 year ago

Hello, So I have a gff3 file where there are lines missing ID (column 9). Those lines mainly concerns CDS' and stop codons. I tried to use "gff3_ID_generator.py" with the command : "python3 gff3_ID_generator.py -g ../../../UK0001.gff3 -og UK0001Mo.gff3" . With UK0001.gff3 being my gff file with missing IDs and UK0001Mo.gff3 being my desired output.

I get this error as the output:

INFO Reading input gff3 file: (../../../UK0001.gff3) INFO Generate new ID for features in (../../../UK0001.gff3) Traceback (most recent call last): File "/home/mestiri/GFF3toolkit/gff3tool/lib/gff3_ID_generator.py", line 333, in main(in_gff=args.gff, merge_report=args.merge_report, out_merge_report=args.out_merge_report, out_gff=args.output_gff, uuid_on=args.universally_unique_identifier, prefix=args.idprefix, digitlen=args.digitlen, report=args.report, alias=args.alias) File "/home/mestiri/GFF3toolkit/gff3tool/lib/gff3_ID_generator.py", line 260, in main if descend['attributes']['ID'] not in ID_dict: KeyError: 'ID'

I don't understand what it means, to be honest. Is there something that I misunderstood concerning this python script ?

Thanks for your help ! Have a nice day !

fmalmeida commented 1 year ago

Hi @MesYosra I think you have mistaken repo names. This script you are using is not related to this repository here. It is related to the GFF3toolkit repo.

MesYosra commented 1 year ago

Hello,

Thanks for your reply. You're right, I made a mistake and I'm really sorry to have bothered you.

Have a nice day !