GFF3 simplifier refactoring and tests #332

MatBarba · 2024-03-21T17:10:17Z

Lots of refactoring in the simplifier module with it's company of tests.

JAlvarezJarreta

Quite the work! But nicely done 👍

src/python/tests/gff3/test_extract_annotation.py

src/python/tests/gff3/test_records.py

src/python/tests/gff3/test_restructure.py

src/python/ensembl/io/genomio/gff3/simplifier.py

src/python/tests/gff3/test_simplifier.py

Co-authored-by: J. Alvarez-Jarreta <[email protected]>

JAlvarezJarreta

One tiny docstring update as we are done! 💪

src/python/ensembl/io/genomio/gff3/simplifier.py

Co-authored-by: J. Alvarez-Jarreta <[email protected]>

MatBarba added 30 commits March 21, 2024 16:17

Reorder functions

54048c2

Load exception

a8b44da

Fail type as a set

c912b4a

Move gff loading in record, add test

61fa945

test loading invalid gff3

9dc0eb7

Fixes

4ce2c1c

First test for simplifier

1183164

Add tests for renaming checks

a05e757

Add test for skip_unrecognized option

d168504

Die if non-gene non supported

b20f3eb

Fix: mobile element clean to get source

4c6f09f

Add gff3_feature tests

d446e61

Ignore notimplemented failsafe

c20e69a

format

94a29ac

simple rename test gff

f9364e7

Add lone tests

a562146

Multiple fixes for simplifier

7c65ae6

One method to check 1 feature

3e2cda9

Use same check method

ea71007

Fixes

ae53317

Test lone CDS, fix make basic IDs

4b00565

Remove lone* from main gff3

2322d2a

support CDS pseudo

f3b22eb

Rearrange mobile element code

bd3a4f1

Add mobile tests + fixes

761d222

Test product if any

2eda364

Fixes

5b9b6b0

Move test files in subfolders

e12d328

Show file name in diff

4f6d7ee

Add clean_gene tests

75d4429

MatBarba added 13 commits March 26, 2024 16:20

More checks, improve code

e99cdf7

Remove obsolete methods

617f77e

format

42f1edd

Merge branch 'mbarba/hack/gff_simplifier' into mbarba/hack/gff_mirna

70fcae0

More tests

245d91f

Test miRNA split support

cb5221b

Add pseudogene check

36022b2

Add pseudogene miRNA

412f59b

Reorganize miRNA test files

230de4e

Fix: no change, don't return modified gene

9803dd1

Merge branch 'hackathon/feb24' into mbarba/hack/gff_simplifier

acf8e61

Bugfix: properly store annotation for translations

4a5f251

Add test for fix

61ffb3f

JAlvarezJarreta requested changes Apr 12, 2024

View reviewed changes

JAlvarezJarreta and others added 11 commits April 12, 2024 16:06

simplify code to avoid using flags

40ea4e6

Restrict what is in the with section

c926678

unify test_from_gff

5469ba7

Restrict with

a6033ef

simp creation outside with

58cf4c3

tmp_dir -> tmp_path

aae6246

Apply suggestions from code review

3f89211

Co-authored-by: J. Alvarez-Jarreta <[email protected]>

Typo

d410b98

Update doc

a948a90

Exception instead of None for simpler_gff3_feature

a05f1de

check_one_feature no return

2195607

MatBarba requested a review from JAlvarezJarreta April 12, 2024 17:33

JAlvarezJarreta approved these changes Apr 15, 2024

View reviewed changes

src/python/ensembl/io/genomio/gff3/simplifier.py Outdated Show resolved Hide resolved

Update src/python/ensembl/io/genomio/gff3/simplifier.py

efa874b

Co-authored-by: J. Alvarez-Jarreta <[email protected]>

MatBarba merged commit d2e085f into hackathon/feb24 Apr 15, 2024
1 check passed

MatBarba deleted the mbarba/hack/gff_simplifier branch April 15, 2024 10:18

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GFF3 simplifier refactoring and tests #332

GFF3 simplifier refactoring and tests #332

MatBarba commented Mar 21, 2024

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JAlvarezJarreta left a comment

GFF3 simplifier refactoring and tests #332

GFF3 simplifier refactoring and tests #332

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MatBarba commented Mar 21, 2024

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