Can't download gff3 files when running in --recursive mode.

[ewilbanks]

Hi folks,

Thanks so much for this awesome tool. LOVE IT. I'm having the following issue when trying to recursively download GFF3 files from a WGS record.

$ ncbi-acc-download --recursive ALVJ00000000.1 -F gff3 -o ALVJ00000000.1.gff
Traceback (most recent call last):
  File "/opt/miniconda3/bin/ncbi-acc-download", line 10, in <module>
    sys.exit(main())
  File "/opt/miniconda3/lib/python3.9/site-packages/ncbi_acc_download/__main__.py", line 66, in main
    download_to_file(dl_id, config, filename, append)
  File "/opt/miniconda3/lib/python3.9/site-packages/ncbi_acc_download/core.py", line 131, in download_to_file
    _validate_and_write(r, fh, dl_id, config)
  File "/opt/miniconda3/lib/python3.9/site-packages/ncbi_acc_download/core.py", line 175, in _validate_and_write
    downloaded = download_wgs_parts(handle, config)
  File "/opt/miniconda3/lib/python3.9/site-packages/ncbi_acc_download/wgs.py", line 102, in download_wgs_parts
    records = list(SeqIO.parse(handle, config.format))
  File "/opt/miniconda3/lib/python3.9/site-packages/Bio/SeqIO/__init__.py", line 609, in parse
    raise ValueError("Unknown format '%s'" % format)
ValueError: Unknown format 'gff3'

I can download the genbank and fasta files recursively for this entry without an issue. I can also download the gff3 files for an individual accession under this WGG entry. For example, the following worked just fine.

ncbi-acc-download ALVJ01000001.1 -F gff3 -o ALVJ00000000.1.gff

Thoughts on how to trouble shoot this?

Thanks!
Lizzy