ncbi-genome-download
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Metagenomes is not a valid group in refseq
As the title states the group metagenomes is not a RefSeq category (yet). Currently requesting it will result in an 404 error and an endless loop (at least no termination)
$ ncbi-genome-download -F fasta -s refseq --retries 3 --parallel 10 --no-cache --verbose --debug -o genomes metagenomes
DEBUG: Checking for a cached summary file
DEBUG: Downloading summary for 'refseq'/'metagenomes' uri: 'https://ftp.ncbi.nih.gov/genomes'
DEBUG: Starting new HTTPS connection (1): ftp.ncbi.nih.gov:443
DEBUG: https://ftp.ncbi.nih.gov:443 "GET /genomes/refseq/metagenomes/assembly_summary.txt HTTP/1.1" 404 None
I tried to make an exception for it, but could not find a smart location to do so. Basically all that's needed is to
if section == "refseq" and group == "metagenomes":
raise ValueError("Unsupported group in refseq: {}".format(group))
Maybe this can be fixed