Problem with "gff3_ID_generator.py"

[MesYosra]

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 !

[mpoelchau]

@MesYosra Sorry about the issues. Are you able to share a snippet (or all) of the gff3 so I can debug? Thanks!

[MesYosra]

Thank you for your reply @mpoelchau. I am sending you the gff ziper file. UK0001.zip

[MesYosra]

@mpoelchau Please, Should I add a header ?

[mpoelchau]

Thanks for sharing the file @MesYosra. I am not sure why this is not working for you. The -uuid option works (instead of the -diglen + -idpre options) - will this help you move forward in the meantime, while I investigate the problem?

[MesYosra]

Thank you for your reply @mpoelchau .When I tried with the option (-uuid ) , it worked but it just changed column 10 (parent) but where there was no ID, there is not yet. Thank you and sorry for the inconvenience

[mpoelchau]

I ran the program as follows with the file that you provided, and obtained the attached output. I am not sure why it didn't add IDs in your case. Were there any other error messages from the program?

$ python -V
Python 3.7.4
$ python repos/GFF3toolkit/gff3tool/lib/gff3_ID_generator.py -g UK0001.gff3 -uuid -og UK-ids.gff3
INFO     Reading input gff3 file: (UK0001.gff3)
INFO     Generate new ID for features in (UK0001.gff3)
INFO     Write out gff3 file: (UK-ids.gff3)
$

UK-ids.gff3.gz

[MesYosra]

Hello, thank you for your time. Yes it works, sorry I didn't see that he put the ID after the parent. Please, is it possible to keep the ID and the parent the same way it is in the base file. Thank you @mpoelchau

[mpoelchau]

@MesYosra sorry, we don't have enough people right now to support this. Perhaps you could ask the Braker developers to support providing IDs for all feature types.