openvax / topiary / 24244257862

85%

master: 90%

Build Type

Pull #105

github

Committed by iskandr

Commit Message

Add expression data loading as DSL fields

New generic expression loader replaces Cufflinks-specific RNA flags.
Expression values become DataFrame columns accessible in --ranking
and --rank-by via the expression DSL.

New CLI flags:
- --gene-expression [name:]file[:id_col[:val_col]] (joins on gene_id)
- --transcript-expression (joins on transcript_id)
- --variant-expression (joins on variant — for isovar output etc.)
Auto-detects Salmon, Kallisto, RSEM, StringTie, Cufflinks formats.

Core changes:
- expression_loader.py: generic loader with format detection
- predictor.py: reorder annotation before ranking so expression
  columns are available to filters; add expression_data parameter
  and _attach_expression_data join logic
- ranking.py: unknown identifiers in parser fall back to Column(),
  so gene_tpm works without column() wrapper
- cli/rna.py: new add_expression_args, deprecate old --rna-* flags

Tests: 571 total (31 new for expression loading + integration)

Pull Request Pull Request #105: Expression data as DSL fields: --gene-expression, --transcript-expression, --variant-expression

Coverage Stats

144 of 214 new or added lines in 6 files covered. (67.29%)

3 existing lines in 1 file now uncovered.

1927 of 2221 relevant lines covered (86.76%)

2.6 hits per line