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feat: add feature_type to var df during add labels step #1006

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merged 9 commits into from
Sep 12, 2024

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Reason for Change

Changes

  • derive feature_type from GENCODE files during gene_processing.py, per rules outlined in issue description
  • re-run gene_processing to update gencode files to pick up feature_type in generated gencode CSVs
  • in write-labels command of cellxgene-schema package, read the feature_type from these CSVs for each feature in the var df and annotate the "feature_type" column with these values.

Notes for Reviewer

  • this PR is pointing to merge against nayib/update-feature-length as a base branch to avoid conflicts around regenerating the gencode CSV files (both PRs require regenerating). End result of schema 5.2 updates should be the CSVs generated in this PR, which encompasses both sets of changes.

Base automatically changed from nayib/update-feature-length to main September 12, 2024 13:47
# Conflicts:
#	cellxgene_schema_cli/cellxgene_schema/gencode_files/genes_mus_musculus.csv.gz
#	cellxgene_schema_cli/tests/fixtures/examples_validate.py
@nayib-jose-gloria nayib-jose-gloria enabled auto-merge (squash) September 12, 2024 13:57
@nayib-jose-gloria nayib-jose-gloria merged commit 39b43aa into main Sep 12, 2024
7 of 8 checks passed
@nayib-jose-gloria nayib-jose-gloria deleted the nayib/add-feature-type branch September 12, 2024 14:07
@nayib-jose-gloria nayib-jose-gloria restored the nayib/add-feature-type branch September 12, 2024 14:09
@nayib-jose-gloria nayib-jose-gloria deleted the nayib/add-feature-type branch October 23, 2024 19:51
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2 participants