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ENH: add fetch-busco-db action and update evaluate-busco accordingly #143

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wants to merge 21 commits into from
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ENH: add fetch-busco-db action and update evaluate-busco accordingly #143

wants to merge 21 commits into from

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Sann5
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@Sann5 Sann5 commented Feb 27, 2024 •
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What's new

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Run it locally

  1. Assuming you already have a local copy of q2-moshpit that is installed in your virtual environment.
cd q2-moshpit
gh pr checkout 143
  1. Let's get you some data to play with:
cd <download here>
qiime moshpit fetch-busco-db --p-virus False --p-prok True --p-euk False --o-busco-db busco_prok_db.qza --verbose
wget https://polybox.ethz.ch/index.php/s/slGyW1uQbyxmyb9/download -O mags.qza
  1. Test it out!
qiime moshpit evaluate-busco --i-bins mags.qza --i-busco-db busco_prok_db.qza --p-lineage-dataset bacteria_odb10 --o-visualization busco.qzv --verbose --p-cpu 6
qiime tools view busco.qzv

Running the tests

pytest -W ignore -vv --pyargs q2_moshpit

Sann5 added 19 commits January 25, 2024 14:04
@Sann5
add fetch-busco-db action
8f97797
@Sann5
Add initializing parameters to BuscoDatabaseDirFmt
7cc427b
@Sann5
Style adjustments to fetch_busco_db
20babd5
@Sann5
add tests for fetch_busco_db
dd404f4
@Sann5
update evaluate-busco
a8dbbcb
@Sann5
Add functionality for the lineage_dataset parameter with TypeMap
69171ef
@Sann5
Adjust fetch_busco_db to run with "all"
981112f
@Sann5
Remove the lineage dataset parameter from TypMap and associated code.
02a4a31
@Sann5
working implementation of type maps
9a57d65
@Sann5
Add comments and change placeholder type in type map
4c256b2
@Sann5
Add lineage check and flag check when db and lineage datasets are not…
7ec51c2 
… none
@Sann5
Erase duplicate parameter modification
cc44a0f
@Sann5
adjust test from fetch busco
012a174
@Sann5
add tests
b945ca8
@Sann5
Removed TypeMap to make it work
270d357
@Sann5
download busco dataset to temporary file
d43d345
@Sann5
now it brakes. variables in method registration
c92ca23
@Sann5
Merge branch 'main' into fetch_busco_db_iss_122
f610a14
@Sann5
enhance busco test
17b94c1
@Sann5 Sann5 added the enhancement New feature or request label Feb 27, 2024
@Sann5 Sann5 requested a review from misialq February 27, 2024 10:08
@Sann5 Sann5 self-assigned this Feb 27, 2024
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github-actions bot commented Feb 27, 2024 •
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This PR/issue depends on:

@misialq
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misialq commented May 1, 2024

Same here, please update with changes from #148, @Sann5 🙏

@Sann5 Sann5 mentioned this pull request May 10, 2024
Merged
@Sann5 Sann5 closed this May 13, 2024
@Sann5 Sann5 deleted the fetch_busco_db_iss_122 branch May 13, 2024 13:23
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ENH: add fetch-busco-db action and update evaluate-busco accordingly
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