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Metagenomes is not a valid group in refseq #115

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openpaul opened this issue Mar 12, 2020 · 0 comments
Open

Metagenomes is not a valid group in refseq #115

openpaul opened this issue Mar 12, 2020 · 0 comments

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@openpaul
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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

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