ERROR in getAnnoFastaFromJoingenes.py: The sequence data given to a Seq object should be a string (not another Seq object etc)

[reubwn]

Hello,

When running the script getAnnoFastaFromJoingenes.py at the end of the BRAKER3 pipeline I'm seeing an error:

ERROR in file braker.pl at line 8515
Failed to execute: python3 getAnnoFastaFromJoingenes.py -g genome.fa -f augustus.hints.gtf -o augustus.hints 1> getAnnoFastaFromJoingenes.augustus.hints_tmp.stdout 2>getAnnoFastaFromJoingenes.augustus.hints_tmp.stderr

Details from the error file:

Traceback (most recent call last):
  File "getAnnoFastaFromJoingenes.py", line 165, in <module>
    codingseq[tx].seq += Seq(record.seq[cds_line['start'] -
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/anaconda3/envs/braker3/lib/python3.12/site-packages/Bio/Seq.py", line 95, in __init__
    raise TypeError(
TypeError: The sequence data given to a Seq object should be a string (not another Seq object etc)

It seems like a simple fix, editing line 165 in getAnnoFastaFromJoingenes.py to pass a string to Seq using str, i.e.

codingseq[tx].seq += Seq(str(record.seq[cds_line['start'] -

Executing the above command then completes without error.

I can see that a similar edit was made to line 153 a few months ago, so posting here in case there are other instances of this elsewhere that might need adjusting.

Cheers, reubwn