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allow handling of compressed SILVA files. #31

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mikerobeson opened this issue Jun 4, 2020 · 1 comment · Fixed by #35
Closed

allow handling of compressed SILVA files. #31

mikerobeson opened this issue Jun 4, 2020 · 1 comment · Fixed by #35

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@mikerobeson
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Many of the files we parse from SILVA, to generate QIIME compatible, taxonomy classifiers, are provided as gzipped files here. It appears that RESCRIPt is unable to process these files unless they are decompressed prior to import into QIIME.

@nbokulich
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right now I'm thinking either:

  1. this could be fixed with add method to automatically download data files from SILVA #28
  2. we make a snakemake workflow related to add pipeline to generate, format, filter SILVA database #29 that could include optionally gunzipping inputs

for the time being, it is not unreasonable to expect users to gunzip files themselves before importing to the appropriate types. Inconvenient but something a user does once so not a big deal...

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