Biodomains semicolon update #124
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…embl IDs, and edited the tests to test that case
…ile, made it more generic, updated its test, plus sonarcloud delinting
… bumped version of gene_table_merged to the new file
jaclynbeck-sage
commented
Feb 21, 2024
| @@ -110,7 +110,6 @@ def rename_columns(df: pd.DataFrame, column_map: dict) -> pd.DataFrame: | |||
| df.rename(columns=column_map, inplace=True) | |||
| except TypeError: | |||
| print("Column mapping must be a dictionary") | |||
| return df | |||
|
|
|||
There was a problem hiding this comment.
I deleted this "return df" statement because SonarCloud complained about it: the function always returns df whether there's an error or not.
jaclynbeck-sage
commented
Feb 21, 2024
| " df=df, split_field=\"ensembl_id\", delim=\";\"\n", | ||
| " )\n", | ||
| " file_ensembl_ids = df[\"ensembl_id\"].drop_duplicates()\n", | ||
| "\n", |
There was a problem hiding this comment.
The chunk of code above is the only relevant code change in this notebook. Everything else is either formatting or different output being displayed.
BWMac
approved these changes
Feb 21, 2024
|
|
Closing this PR without merging. They changed the biodomains file format back to the old format (one Ensembl ID per row), so this update is no longer needed. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR addresses AG-1366 and AG-1371.
The new biodomains file changed the format of their
ensembl_idcolumn, so that instead of a single Ensembl ID per row, some rows have strings like this: "ENSG0001;ENSG0002;ENSG0003" while most still have a single ID per row. To account for this change I did the following:utils.pycalledsplit_delimited_field_to_multiple_rows, which will take each row with multiple Ensembl IDs, duplicate it so there's enough rows for all the IDs in the list, and then assign a single Ensembl ID per row. This function is written to be generic.test_utils.pygenes_biodomainsandgene_info) call this util function to expand out the biodomains dataframe before doing more processing on itgenes_biodomainsto have some input with semicolon-delimited listsgene_metadatafile and bumped the version of it from 10 to 11 in the configs.There are also several places in the code where I did de-linting to make SonarCloud happy.