Incorporate uniprot id into gene info #160

beatrizsaldana · 2024-11-23T00:12:54Z

AG-1392 - Incorporate uniprot ID into gene_info

Adding uniprotkb_accessions column to the gene_info dataset using the uniprot to ensembl mapping file (syn54113663).

Changes

Updated config.yaml and test_config.yaml to include the uniprot mapping dataset
Updated existing gene_info tests to include a uniprotkb_accessions column
Updated gene_info output assets to include a uniprotkb_accessions column
Added ensg_to_uniprot_mapping_good.tsv to the gene_info testing assets
Added gx validation for the uniprotkb_accessions column

BWMac

Is the commented out regex GX expectation still meant to be there? - If you wanted to check if the list members matched this regex you could do that by treating the field as nested and using a JSON schema validation expectation.

config.yaml

test_config.yaml

JessterB

Pre-approving this, but please add the file version number in the four places Brad flagged. Otherwise we will default to whatever the latest version of the file is, and that can result in unexpected data surprises and murky provenance...

config.yaml

tests/test_assets/gene_info/input/ensg_to_uniprot_mapping_good.tsv

…test_config

src/agoradatatools/etl/transform/gene_info.py

jaclynbeck-sage · 2024-11-25T19:44:45Z

tests/transform/test_gene_info.py

+        output_df = gene_info.add_uniprot_id_to_gene_info(gene_info_df, uniprot_df)
+
+        # Read in expected dataframe and convert uniprotkb_accessions to list
+        expected_df = pd.read_csv(


Matter of opinion (so, optional): It might be cleaner to save the expected output as a json file so no conversion code is needed.

So true, I like your suggestion better than what I implemented, thank you!

tests/transform/test_gene_info.py

src/agoradatatools/etl/transform/gene_info.py

tests/transform/test_gene_info.py

gx_suite_definitions/gene_info.ipynb

jaclynbeck-sage

Needs a little bit of moving code around but it's almost there!

…base

…testing files.

jaclynbeck-sage · 2024-11-25T22:38:48Z

tests/transform/test_gene_info.py

@@ -227,6 +233,23 @@ class TestTransformGeneInfo:
        "Fail with bad data type in tep_adi_info's is_adi column",
        "Fail with bad data type in tep_adi_info's is_tep column",
    ]
+    unpiprot_input_files = {


I think this section goes away since the test for the function no longer exists?

Can you confirm if this section should go away, or stay?

tests/test_assets/gene_info/input/geneinfo_uniprot_good.csv

jaclynbeck-sage

Just cleanup of unused variables and files for testing, everything else looks great!

BWMac

🚀 Pre-approving pending finishing up Jaclyn's comments

sonarqubecloud · 2024-11-27T21:41:44Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

jaclynbeck-sage

Looks good, approved!

Beatriz Saldana added 12 commits November 13, 2024 14:34

Added uniprotkb_accession column to gene_info dataset

686002a

Updated gx validation for gene_info

deb689d

Added the uniprot mapping file to the gene_info provenance

f7c4ec0

Updating gx validation

d331fe2

Updated gx validation to include uniprotkb_accessions

ab79e49

Finally got the gx validation to use the plural uniprotkb_accessions

c18dff5

Pytests passing

ea0efc9

Removed rename_unknown_column() and related code

1630434

gene_info test_add_uniprot_id_to_gene_info_should_pass passing

5702c82

uniprot fail test is failing

c0f6bee

Removing testing yaml file that we do not need

74a52cc

Removing unnecessary changes to utils.py

3f0a9fa

beatrizsaldana marked this pull request as ready for review November 23, 2024 00:19

beatrizsaldana requested a review from a team as a code owner November 23, 2024 00:19

BWMac reviewed Nov 25, 2024

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JessterB approved these changes Nov 25, 2024

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Updated version number of syn54113663 to syn54113663.3 in config and …

49b1f74

…test_config

beatrizsaldana requested a review from BWMac November 25, 2024 19:36

jaclynbeck-sage reviewed Nov 25, 2024

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Made the ensembl to uniprot test mapping file smaller

88132b4

beatrizsaldana requested a review from jaclynbeck-sage November 25, 2024 19:52

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Beatriz Saldana added 2 commits November 25, 2024 13:37

Improved uniprot code integration with expected flow of existing code…

ea0aeab

…base

Removed unused regex for uniprot gx validation

932e15c

Beatriz Saldana added 2 commits November 25, 2024 13:44

Adding duplicate ensembl ID to uniprot testing file. Removing unused …

628c346

…testing files.

Updating testing_gene_info docstring

27588b8

beatrizsaldana requested a review from jaclynbeck-sage November 25, 2024 21:47

jaclynbeck-sage reviewed Nov 25, 2024

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jaclynbeck-sage requested changes Nov 25, 2024

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Removed unused testing file

4864f82

beatrizsaldana requested a review from jaclynbeck-sage November 26, 2024 20:07

BWMac approved these changes Nov 27, 2024

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Removed unused variables in gene_info testing script

d359604

jaclynbeck-sage approved these changes Nov 27, 2024

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beatrizsaldana merged commit ae4cf82 into dev Nov 27, 2024
9 checks passed

beatrizsaldana deleted the beatrizsaldana/AG-1392/ADT-Incorporate-uniprot-ID-into-gene_info branch December 2, 2024 18:58

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Incorporate uniprot id into gene info #160

Incorporate uniprot id into gene info #160

beatrizsaldana commented Nov 23, 2024 •

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Incorporate uniprot id into gene info #160

Incorporate uniprot id into gene info #160

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beatrizsaldana commented Nov 23, 2024 • edited Loading

AG-1392 - Incorporate uniprot ID into gene_info

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beatrizsaldana commented Nov 23, 2024 •

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