Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Open
wants to merge 15 commits into
base: master
Choose a base branch
from
Open

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

wants to merge 15 commits into from

Conversation

heracle
Copy link
Collaborator

@heracle heracle commented Aug 2, 2021 •
edited
Loading

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 [email protected]

@heracle heracle requested review from hmusta and karasikov August 2, 2021 12:52
karasikov
karasikov requested changes Aug 31, 2021
View reviewed changes
metagraph/tests/annotation/taxonomy/test_taxonomy.cpp Outdated Show resolved Hide resolved
metagraph/tests/annotation/taxonomy/test_taxonomy.cpp Outdated Show resolved Hide resolved
metagraph/tests/annotation/taxonomy/test_taxonomy.cpp Outdated Show resolved Hide resolved
metagraph/src/annotation/taxonomy/tax_classifier.cpp Outdated Show resolved Hide resolved
metagraph/src/annotation/taxonomy/tax_classifier.cpp Outdated Show resolved Hide resolved
metagraph/src/annotation/taxonomy/tax_classifier.cpp Outdated Show resolved Hide resolved
metagraph/src/annotation/taxonomy/tax_classifier.cpp Outdated Show resolved Hide resolved
metagraph/src/annotation/taxonomy/tax_classifier.cpp Outdated Show resolved Hide resolved
metagraph/src/annotation/taxonomy/tax_classifier.cpp Outdated Show resolved Hide resolved
metagraph/src/annotation/taxonomy/tax_classifier.cpp Outdated Show resolved Hide resolved
@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 <[email protected]>
@heracle
address comments
f2ac8c7
@heracle
add some small methods that will be further used for tax class
ea9ffa5 
Signed-off-by: Radu Muntean <[email protected]>
@heracle
add data files used for taxonomic integration and unit tests
8efaa33 
Signed-off-by: Radu Muntean <[email protected]>
@heracle
rebase
afa99ff
@heracle
taxonomic classification skeleton with the RMQ preprocessing
62e3107 
Signed-off-by: Radu Muntean <[email protected]>
@heracle
address comments
865e69e 
Signed-off-by: Radu Muntean <[email protected]>
@heracle
delete tax test files
29361f6 
Signed-off-by: Radu Muntean <[email protected]>
@heracle
small reformat
76f3c21 
Signed-off-by: Radu Muntean <[email protected]>
@heracle
add some small methods that will be further used for tax class
b83d72f 
Signed-off-by: Radu Muntean <[email protected]>
@heracle
address comments
e3ce8f6
@heracle
implement the taxonomic classification with queries on the annotation…
a9df695 
… matrix

Signed-off-by: Radu Muntean <[email protected]>
@heracle
address review & rebase
e4eaf4a 
Signed-off-by: Radu Muntean <[email protected]>
@heracle
minor
c3117f1 
Signed-off-by: Radu Muntean <[email protected]>
@heracle heracle force-pushed the mtg_taxclass_4 branch 4 times, most recently from d93dd4d to ee58d8e Compare September 14, 2021 11:29
@heracle
Copy link
Collaborator Author

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
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@hmusta hmusta Awaiting requested review from hmusta

@karasikov karasikov Awaiting requested review from karasikov

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@heracle @karasikov