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[MRG] add 'sourmash signature' signature manipulation utilities. #587

Merged
merged 52 commits into from
Jan 8, 2019
Merged

[MRG] add 'sourmash signature' signature manipulation utilities. #587

merged 52 commits into from
Jan 8, 2019

Commits on Dec 26, 2018

  1. initial setup for 'sourmash signature' command line

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    ctb committed Dec 26, 2018
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  2. fix module name sourmash_lib -> sourmash

    @ctb
    ctb committed Dec 26, 2018
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  3. fix module name sourmash_lib -> sourmash

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    ctb committed Dec 26, 2018
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  4. fix module name sourmash_lib -> sourmash

    @ctb
    ctb committed Dec 26, 2018
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  5. fix module name sourmash_lib -> sourmash

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    ctb committed Dec 26, 2018
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  6. adjust tests and test filenames to be explicit

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    ctb committed Dec 26, 2018
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  7. initial merge and intersect functionality

    @ctb
    ctb committed Dec 26, 2018
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  8. add merge, intersect, and rename

    @ctb
    ctb committed Dec 26, 2018
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  9. added subtract, extract, and downsample

    @ctb
    ctb committed Dec 26, 2018
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  10. added moltype and ksize

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    ctb committed Dec 26, 2018
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  11. add -o options

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    ctb committed Dec 26, 2018
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Commits on Dec 27, 2018

  1. added documentation, refactored sourmash sig extract a bit.

    @ctb
    ctb committed Dec 27, 2018
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  2. spell check new documentation :)

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    ctb committed Dec 27, 2018
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  3. add --md5 and --name selectors to sourmash sig extract; update tests,… 

    … docs
    @ctb
    ctb committed Dec 27, 2018
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  4. Merge branch 'master' of github.com:dib-lab/sourmash into add/signatu… 

    …re_subcommand_2
    @ctb
    ctb committed Dec 27, 2018
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  5. add 'info' command

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    ctb committed Dec 27, 2018
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  6. Merge branch 'master' into add/signature_subcommand_2

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    ctb committed Dec 27, 2018
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Commits on Dec 28, 2018

  1. Merge branch 'master' into add/signature_subcommand_2

    @ctb
    ctb committed Dec 28, 2018
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  2. adjust tests to ensure that full signatures are identical

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    ctb committed Dec 28, 2018
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Commits on Dec 29, 2018

  1. start thinking about abundance stuff

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    ctb committed Dec 29, 2018
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Commits on Dec 30, 2018

  1. Merge branch 'master' of github.com:dib-lab/sourmash into add/signatu… 

    …re_subcommand_2
    @ctb
    ctb committed Dec 30, 2018
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  2. fix merge/intersect behavior with respect to abund, add some tests

    @ctb
    ctb committed Dec 30, 2018
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  3. add a flatten command

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    ctb committed Dec 30, 2018
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  4. make sure subtract breaks on --track-abundance signatures

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    ctb committed Dec 30, 2018
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Commits on Dec 31, 2018

  1. add import/export

    @ctb
    ctb committed Dec 31, 2018
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  2. add py27 compat print foo

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    ctb committed Dec 31, 2018
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  3. add --num to downsample

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    ctb committed Dec 31, 2018
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Commits on Jan 1, 2019

  1. update sourmash main doc

    @ctb
    ctb committed Jan 1, 2019
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  2. num to scaled conversion

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    ctb committed Jan 1, 2019
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  3. add conversion from scaled to num

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    ctb committed Jan 1, 2019
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  4. make downsample work on multisig files

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    ctb committed Jan 1, 2019
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Commits on Jan 3, 2019

  1. fix headings in sourmash sig docs

    @ctb
    ctb committed Jan 3, 2019
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  2. add sourmash signature overlap

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    ctb committed Jan 3, 2019
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  3. Merge branch 'master' of github.com:dib-lab/sourmash into add/signatu… 

    …re_subcommand_2
    @ctb
    ctb committed Jan 3, 2019
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Commits on Jan 4, 2019

  1. Merge branch 'master' into add/signature_subcommand_2

    @ctb
    ctb committed Jan 4, 2019
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Commits on Jan 5, 2019

  1. Merge branch 'master' of github.com:dib-lab/sourmash into add/signatu… 

    …re_subcommand_2
    @ctb
    ctb committed Jan 5, 2019
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  2. add missing subcommands to docs, output

    @ctb
    ctb committed Jan 5, 2019
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  3. fix typo

    @taylorreiter
    taylorreiter committed Jan 5, 2019
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Commits on Jan 7, 2019

  1. make sure 'sourmash sig info' prints to stdout not stderr

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    ctb committed Jan 7, 2019
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  2. minor comment update

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    ctb committed Jan 7, 2019
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  3. merge now supports multiple signatures per file; add merge --flatten … 

    …flag
    @ctb
    ctb committed Jan 7, 2019
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  4. added support for multiple signatures in one file to both intersect a… 

    …nd subtract
    @ctb
    ctb committed Jan 7, 2019
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  5. added multisig tests for everything but flatten

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    ctb committed Jan 7, 2019
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  6. added more multisig tests, and added --flatten to subtract

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    ctb committed Jan 7, 2019
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  7. Merge branch 'master' of github.com:dib-lab/sourmash into add/signatu… 

    …re_subcommand_2
    @ctb
    ctb committed Jan 7, 2019
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  8. adjust test to use last_result

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    ctb committed Jan 7, 2019
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  9. revamp --quiet and --debug handling in lca submodule

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    ctb committed Jan 7, 2019
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  10. fix py2 division bug **caught by tests and CI**

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    ctb committed Jan 7, 2019
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  11. fix errors introduced by debug revamp in lca :)

    @ctb
    ctb committed Jan 7, 2019
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Commits on Jan 8, 2019

  1. rename sig info to sig describe

    @ctb
    ctb committed Jan 8, 2019
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  2. deal more nicely with signature loading errors in describe()

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    ctb committed Jan 8, 2019
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  3. isolate black magic functionality

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    ctb committed Jan 8, 2019
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