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Create tests for feature importing #429

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garrettjstevens opened this issue Aug 28, 2024 · 1 comment · Fixed by #441
Closed

Create tests for feature importing #429

garrettjstevens opened this issue Aug 28, 2024 · 1 comment · Fixed by #441
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@dariober

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@garrettjstevens
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Create tests to make sure that gff3ToAnnotationFeature gives us consistent results for various types of GFF3 input.

These tests were mentioned in #381, but have now been split off into a different issue.
@garrettjstevens
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@dariober I had an idea for comparing features with nested children. Basically it involves converting children from an object to an array, and then using chai's deepEqualExcludingEvery to compare the features excluding _id. Check out 08590d4 in the test_compare_annotation_children branch.

dariober added a commit that referenced this issue Sep 10, 2024
@dariober
Tests for feature conversion (#429)
149a434 
Test `Convert example 3` fails because there should be 4 CDSs in the
converted feature object but current code detects 3

Test `Convert braker gff` fails because the converted feature includes
intron, start_codon, and stop_codon
garrettjstevens pushed a commit that referenced this issue Sep 20, 2024
@dariober @garrettjstevens
Tests for feature conversion (#429)
58e456c 
Test `Convert example 3` fails because there should be 4 CDSs in the
converted feature object but current code detects 3

Test `Convert braker gff` fails because the converted feature includes
intron, start_codon, and stop_codon
@garrettjstevens garrettjstevens linked a pull request Sep 20, 2024 that will close this issue
Add feature import conversion tests #441
Merged
garrettjstevens added a commit that referenced this issue Sep 21, 2024
@dariober @garrettjstevens
Add feature import conversion tests (#441)
1b94250 
* Temp commit

* Use chai to deeply compare annotation features

* Some working tests

* Fix import

* Tests for feature conversion (#429)

Test `Convert example 3` fails because there should be 4 CDSs in the
converted feature object but current code detects 3

Test `Convert braker gff` fails because the converted feature includes
intron, start_codon, and stop_codon

* Fix linter

* Fix CDS overlap calculation

* Ignore more calculated properties on conversion

---------

Co-authored-by: Garrett Stevens <stevens.garrett.j@gmail.com>
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Add feature import conversion tests GMOD/Apollo3
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@dariober @garrettjstevens