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implement the taxonomic classification with queries on the annotation matrix#347

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heracle wants to merge 15 commits intomasterfrom
mtg_taxclass_4
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implement the taxonomic classification with queries on the annotation matrix#347
heracle wants to merge 15 commits intomasterfrom
mtg_taxclass_4

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@heracle heracle commented Aug 2, 2021 •
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Implement:

  • Taxonomic Classification on the fly by iterating the annotation matrix
  • LCA computation
  • update_scores_and_lca
  • unit tests
  • tax class CLI
  • integration tests

Testing workflow:

python3 ../integration_tests/main.py --test_filter "test_taxonomy_"

./unit_tests --gtest_filter=TaxonomyTest.ClsAnno_ClassifierUpdateScoresAndLca && ./unit_tests --gtest_filter=TaxonomyTest.ClsAnno_KmerToTaxidUpdate && ./unit_tests --gtest_filter=TaxonomyTest.ClsAnno_FindLca && ./unit_tests --gtest_filter=TaxonomyTest.ClsAnno_RmqPreprocessing && ./unit_tests --gtest_filter=TaxonomyTest.ClsAnno_DfsStatistics

Signed-off-by: Radu Muntean radu.muntean.2@gmail.com

@heracle heracle requested review from hmusta and karasikov August 2, 2021 12:52
karasikov
karasikov requested changes Aug 31, 2021
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@heracle heracle marked this pull request as draft September 2, 2021 08:23
Base automatically changed from mtg_taxclass_3 to master September 6, 2021 08:26
heracle added 14 commits September 9, 2021 11:43
@heracle
add some small methods that will be further used for tax class
468c59a 
Signed-off-by: Radu Muntean <radu.muntean.2@gmail.com>
@heracle
address comments
f2ac8c7
@heracle
add some small methods that will be further used for tax class
ea9ffa5 
Signed-off-by: Radu Muntean <radu.muntean.2@gmail.com>
@heracle
add data files used for taxonomic integration and unit tests
8efaa33 
Signed-off-by: Radu Muntean <radu.muntean.2@gmail.com>
@heracle
rebase
afa99ff
@heracle
taxonomic classification skeleton with the RMQ preprocessing
62e3107 
Signed-off-by: Radu Muntean <radu.muntean.2@gmail.com>
@heracle
address comments
865e69e 
Signed-off-by: Radu Muntean <radu.muntean.2@gmail.com>
@heracle
delete tax test files
29361f6 
Signed-off-by: Radu Muntean <radu.muntean.2@gmail.com>
@heracle
small reformat
76f3c21 
Signed-off-by: Radu Muntean <radu.muntean.2@gmail.com>
@heracle
add some small methods that will be further used for tax class
b83d72f 
Signed-off-by: Radu Muntean <radu.muntean.2@gmail.com>
@heracle
address comments
e3ce8f6
@heracle
implement the taxonomic classification with queries on the annotation…
a9df695 
… matrix

Signed-off-by: Radu Muntean <radu.muntean.2@gmail.com>
@heracle
address review & rebase
e4eaf4a 
Signed-off-by: Radu Muntean <radu.muntean.2@gmail.com>
@heracle
minor
c3117f1 
Signed-off-by: Radu Muntean <radu.muntean.2@gmail.com>
@heracle heracle force-pushed the mtg_taxclass_4 branch 4 times, most recently from d93dd4d to ee58d8e Compare September 14, 2021 11:29
@heracle
rebase master and code reformat
366b99a 
Signed-off-by: Radu Muntean <radu.muntean.2@gmail.com>
@heracle
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heracle commented Sep 14, 2021

Thank you for the review! I have rebased according to master and tried to address all the old comments

@heracle heracle marked this pull request as ready for review September 14, 2021 12:37
@heracle heracle requested a review from karasikov September 14, 2021 19:03
@heracle heracle mentioned this pull request Sep 14, 2021
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@hmusta hmusta Awaiting requested review from hmusta

@karasikov karasikov Awaiting requested review from karasikov

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@heracle @karasikov