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[WIP] CAMI profiling output for sourmash tax #1606

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wants to merge 121 commits into from
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[WIP] CAMI profiling output for sourmash tax #1606

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luizirber
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Based on the krona code.

TODO

  • deal with TaxID/Taxpath, which is not currently registered in LineagePair...

Wishlist

  • The CAMI profiling format contains the same data as BIOM, so it might be possible to convert/support BIOM too

ctb and others added 30 commits May 21, 2021 07:47
@ctb
provide a kind of ridiculous upgrade to lca index to better deal with…
db32c56 
… identifiers/taxonomy
@ctb
update load_taxonomy_assignments to be more flexible and pay attentio…
2c305ed 
…n to CLI
@bluegenes
init structure for taxonomy subcommand
1908205
@bluegenes
more init
494dbbc
@bluegenes
syntax and add tax to init
ac3a553
@bluegenes
Merge branch 'latest' into add-taxonomy
1966afc
@ctb
Merge branch 'latest' into update/lca_index
85ef9fa
@bluegenes
Merge branch 'latest' into add-taxonomy
ce939e5
@bluegenes
init tax tests
208a9b3
@bluegenes
Merge branch 'latest' into update/lca_index
7e822c6
@bluegenes
Merge branch 'update/lca_index' of https://github.com/dib-lab/sourmash …
a5bc6f0 
…into add-taxonomy
@bluegenes
working tax summarize command
33c55f3
@bluegenes
fix main
850e4e4
@bluegenes
init tests for new tax_utils
0029d51
@bluegenes
add ascending taxlist
ea2456a
@bluegenes
init classify cmd
1075b68
@bluegenes
init tax cli testing
88b643b
@bluegenes
Merge branch 'latest' into add-taxonomy
822d664
@bluegenes
fix filename
a26052d
@bluegenes
Merge branch 'add-taxonomy' of https://github.com/dib-lab/sourmash in…
d2fef53 
…to add-taxonomy
@bluegenes
change to function for classify threshold
1448985
@bluegenes
add header
06daba4
@bluegenes
enable single gather result for summarize; mult for classify
bd26822
@taylorreiter
add util script to take output of tax and format for krona viz (#1559)
7b5fc72
@bluegenes
Merge branch 'latest' into add-taxonomy
63be068
@bluegenes
get summarized working for summary and krona output
2c5f864
@bluegenes
init test krona output
c868e06
@bluegenes
add write_summary function
bb04930
@bluegenes
get classify working again, both summary and krona output
4fd6de0
@bluegenes
test write_classification
8d6f321
bluegenes and others added 24 commits June 15, 2021 15:22
@bluegenes
move notify
9c5ff01
@bluegenes
cleanup
13f5f00
@bluegenes
remove tax combine; add tax label
891d951
@bluegenes
verson of load_taxonomy that strictly uses headers
3e330b5
@bluegenes
use new tax fn; enable mult taxonomy inputs
16d5d7f
@bluegenes
Merge branch 'latest' into add-taxonomy
f884010
@bluegenes
init tax docs
f46ab7d
@bluegenes
add classification status to classify output
8a41e94
@bluegenes
add multi db gather test csv
89e448b
@bluegenes
fix typo
86a53f8
@bluegenes
whoops, actually fix
a9366bd
@bluegenes
handle accession in lineage csv header
7044ae5
@bluegenes
fix line width
24bea0f
@bluegenes
return available ranks from load_taxonomy_csv
3cbac9f
@hehouts @bluegenes @ctb
[MRG] add test to confirm failure when summarizing on empty gather (#…
bee47fd 
…1560)

* added summarize on empty gather.csv test

* added empty taxonomy csv test

* fix typo

* Update test_tax.py

* trouble shoot tests

* troubleshooting empty gather test

* fixed, maybe? (#1596)

* trying to pull

* cleaned up test_summarize_empty_gather_tax...

* cleaned test_summarize_empty_gather

* fixed test comments

* removed comment

* Update tests/test_tax.py

Co-authored-by: Tessa Pierce Ward <bluegenes@users.noreply.github.com>

* Update tests/test_tax.py

Co-authored-by: Tessa Pierce Ward <bluegenes@users.noreply.github.com>

* updated empty-gather test

Co-authored-by: Tessa Pierce Ward <bluegenes@users.noreply.github.com>
Co-authored-by: C. Titus Brown <titus@idyll.org>
@bluegenes
init standardize errs
7d41b87
@bluegenes
Merge branch 'add-taxonomy' of https://github.com/sourmash-bio/sourmash…
b0501c2 
… into add-taxonomy
@bluegenes
add good valueerror for empty lineage csv file
643a62c
@bluegenes
better catch errs in __main__; test all cmds: empty gather, lineage f…
43e3609 
…iles
@bluegenes
check available ranks, bad gather headers, empty gather, etc
4b1ded4
@bluegenes
emit one (and only one) warning per 100% match
4fdabb7
@bluegenes
Merge branch 'latest' into add-taxonomy
0e6df72
@bluegenes
add all functions to __all__ ...is this desired?
e495d1d
@luizirber
start cami profiling output based on krona
a0fc0c8
@codecov-commenter
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codecov-commenter commented Jun 18, 2021 •
edited
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Codecov Report

Merging #1606 (a0fc0c8) into add-taxonomy (e495d1d) will increase coverage by 7.74%.
The diff coverage is 81.81%.

Impacted file tree graph

@@               Coverage Diff                @@
##           add-taxonomy    #1606      +/-   ##
================================================
+ Coverage         81.49%   89.23%   +7.74%     
================================================
  Files               110       83      -27     
  Lines             10964     7359    -3605     
  Branches           1318     1350      +32     
================================================
- Hits               8935     6567    -2368     
+ Misses             1794      553    -1241     
- Partials            235      239       +4
Flag Coverage Δ
python 89.23% <81.81%> (+0.05%) ⬆️
rust ?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/sourmash/tax/tax_utils.py 90.72% <81.81%> (-1.14%) ⬇️
src/sourmash/cli/tax/label.py 88.88% <0.00%> (-11.12%) ⬇️
src/sourmash/cli/tax/summarize.py 80.76% <0.00%> (-6.74%) ⬇️
src/sourmash/cli/tax/classify.py 82.75% <0.00%> (-6.14%) ⬇️
src/sourmash/sig/__main__.py 91.50% <0.00%> (-0.19%) ⬇️
src/sourmash/cli/index.py 100.00% <0.00%> (ø)
src/sourmash/cli/gather.py 100.00% <0.00%> (ø)
src/sourmash/cli/search.py 100.00% <0.00%> (ø)
src/sourmash/cli/compare.py 100.00% <0.00%> (ø)
src/sourmash/cli/prefetch.py 100.00% <0.00%> (ø)
... and 40 more

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Base automatically changed from add-taxonomy to latest June 23, 2021 13:58
@bluegenes bluegenes mentioned this pull request Jul 5, 2021
Merged
11 tasks
@luizirber luizirber mentioned this pull request Feb 12, 2023
Merged
@luizirber luizirber closed this Feb 13, 2023
@luizirber luizirber deleted the tax_cami_output branch February 13, 2023 05:03
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6 participants
@luizirber @codecov-commenter @ctb @bluegenes @taylorreiter @hehouts