When trying out the script with bcbio-gff 0.7.0 and biopython 1.81 I get the following error:
python ~/code/GFF-to-GenBank/gff_to_genbank_edit.py results/genome_annotation.gff3 data/reference.fasta
Traceback (most recent call last):
File "/Users/corneliusromer/code/GFF-to-GenBank/gff_to_genbank_edit.py", line 88, in <module>
main(*sys.argv[1:])
File "/Users/corneliusromer/code/GFF-to-GenBank/gff_to_genbank_edit.py", line 25, in main
SeqIO.write(_check_gff(_fix_ncbi_id(_extract_regions(gff_iter))), out_file, "genbank")
File "/opt/homebrew/Caskroom/miniforge/base/envs/py11/lib/python3.11/site-packages/Bio/SeqIO/__init__.py", line 524, in write
count = writer_class(handle).write_file(sequences)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/py11/lib/python3.11/site-packages/Bio/SeqIO/Interfaces.py", line 232, in write_file
count = self.write_records(records, maxcount)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/py11/lib/python3.11/site-packages/Bio/SeqIO/Interfaces.py", line 205, in write_records
for record in records:
File "/Users/corneliusromer/code/GFF-to-GenBank/gff_to_genbank_edit.py", line 47, in _check_gff
if isinstance(rec.seq, Seq.UnknownSeq):
^^^^^^^^^^^^^^
AttributeError: module 'Bio.Seq' has no attribute 'UnknownSeq'
corneliusroemer
commented
11 months ago
When trying out the script with bcbio-gff 0.7.0 and biopython 1.81 I get the following error: