Error in generation of antismash regions using "generate_antismash_gbk.py"

[mfrand-7]

Hi,

I apologise in advance if this is a rather simple question, I am a newbie in this area and my learning process is slow.

I am trying to generate antismash regions from my DeepBGC output. Using the proposed script I manage to convert my first 5 regions. However, for the rest I get this output:

Parsing region coordinates...
CDS ['JJQ97_RS05155'] is not translated (don't have 'translation' qualifier)! translating with BioPython (default transl_table=11 if not filled)..
CDS ['JJQ97_RS05160'] is not translated (don't have 'translation' qualifier)! translating with BioPython (default transl_table=11 if not filled)..
CDS ['JJQ97_RS05165'] is not translated (don't have 'translation' qualifier)! translating with BioPython (default transl_table=11 if not filled)..
CDS ['JJQ97_RS05170'] is not translated (don't have 'translation' qualifier)! translating with BioPython (default transl_table=11 if not filled)..
CDS ['JJQ97_RS05175'] is not translated (don't have 'translation' qualifier)! translating with BioPython (default transl_table=11 if not filled)..
CDS ['JJQ97_RS05180'] is not translated (don't have 'translation' qualifier)! translating with BioPython (default transl_table=11 if not filled)..
CDS ['JJQ97_RS05185'] is not translated (don't have 'translation' qualifier)! translating with BioPython (default transl_table=11 if not filled)..
CDS ['JJQ97_RS05185'] is not translated (don't have 'translation' qualifier)! translating with BioPython (default transl_table=11 if not filled)..
Traceback (most recent call last):
  File "/home/mfrand/.local/lib/python3.8/site-packages/Bio/Seq.py", line 1232, in translate
    table_id = int(table)
TypeError: int() argument must be a string, a bytes-like object or a number, not 'list'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "generate_antismash_gbk.py", line 131, in <module>
    main()
  File "generate_antismash_gbk.py", line 111, in main
    feature.translate(region_gbk).seq]
  File "/home/mfrand/.local/lib/python3.8/site-packages/Bio/SeqFeature.py", line 462, in translate
    return feat_seq.translate(
  File "/home/mfrand/.local/lib/python3.8/site-packages/Bio/SeqRecord.py", line 1320, in translate
    self.seq.translate(
  File "/home/mfrand/.local/lib/python3.8/site-packages/Bio/Seq.py", line 1251, in translate
    raise ValueError("Bad table argument")
ValueError: Bad table argument

My first thought was that there was an error in my coordinates table, however, I am not able to find it as its format seems to be the same as example.csv ( I attached a sample of my table below; starting from the row marked in bold it gives the error). I have tried to modify the script to solve this problem but I haven't been able to do it yet.

#record_name,start_loc,end_loc
NZ_CP068034.2,431183,432377
NZ_CP068034.2,477321,504096
NZ_CP068034.2,505213,506620
NZ_CP068034.2,520667,529185
NZ_CP068034.2,603185,636668
NZ_CP068034.2,1171217,1207238
NZ_CP068034.2,1261449,1269122
NZ_CP068034.2,1277741,1294683
NZ_CP068034.2,1329947,1331198
NZ_CP068034.2,1348002,1372261
NZ_CP068034.2,1631019,1638565

Thank you in advance