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BUG: unzip fasta.gz before validating #244

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@misialq misialq commented May 23, 2020

Solves #194.
Tested against: QIIME 2 Release 2020.2

Gzipped FASTA file will be unzipped (once) before validating and stored on disk. Consequently, the path to the original sequence will be updated with the path to the unzipped sequence.

@nbokulich nbokulich self-requested a review May 23, 2020 14:17
@nbokulich nbokulich self-assigned this May 23, 2020
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Thanks @misialq ! After looking into this, it looks like the original issue (silent failure of gzipped fasta imports) was inadvertently fixed by updates to the format validation. This PR adds enhancement — by unzipping gzipped imports — but _validate_lines is not the best place for this, creating a new GzippedFASTAFormat would probably be a better way to handle this case... now we're talking a whole new can of worms so for the time being, I will just close down this PR. Sorry about the mix-up!

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