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[MRG] implement tax grep to produce identifier picklists from taxonomies #2178

Merged
merged 19 commits into from
Aug 8, 2022
Merged

[MRG] implement tax grep to produce identifier picklists from taxonomies #2178

merged 19 commits into from
Aug 8, 2022

Commits on Aug 4, 2022

  1. add basics of sourmash tax grep command

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  2. initial implementation

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  3. fixed bug; added various args

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Commits on Aug 6, 2022

  1. more tests

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  2. support gzipped taxonomy files

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  3. let 'prepare' save gzip csv files, too

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  4. switch to outputting lineage; refactor

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  5. fix and test invert match

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  6. more tests

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  7. add --count

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  8. comment

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Commits on Aug 7, 2022

  1. upd docs

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  2. add test for tax prepare combining

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  3. test multiple, duplicate tax

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  4. finish? tests

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  5. Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int… 

    …o tax_grep
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  6. implement --force

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  7. update usage string

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Commits on Aug 8, 2022

  1. Update doc/command-line.md 

    Co-authored-by: Tessa Pierce Ward <bluegenes@users.noreply.github.com>
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    ctb and bluegenes authored Aug 8, 2022
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