Update and expand tutorials against real ENCODE data - #51
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The zYe7g6qnyxGDxRd Nextcloud share is no longer live; Mf2zMePGBzFWFk8 is the current working link for the same TutorialsData.zip archive. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
The transcript-context filter variable is trid, not transcript_id. Using transcript_id silently defaults to None, and gene.coverage[:,None] triggers numpy newaxis broadcasting that crashes any()/all() calls on the resulting 2D array -- exactly the ValueError reported in #19. Also corrects 06_filtering.ipynb's cached output, stale since trid was renamed from transcript_id in the library.
The code cell already calls transcript_table(cpm=True); only the cached DataFrame output still showed sum_tpm from before the 2.1.0 tpm->cpm rename. Values are unchanged (cpm was always the correct formula), so only the label needed correcting.
…orial The .tbi index was required for the reference annotation; that requirement was removed for #28 back in 2.0.3 (plain sequential gzip reading, no TabixFile). Also documents infer_genes=True for gtf/gff3 files without explicit gene entries, which may happen when importing files from external tools.
…rials Adds consistent logging setup (matching 03/03b's existing pattern) to 04/05/06/08/09/10, which previously had none -- their warnings were falling through Python's bare last-resort handler with no level prefix. All 8 notebooks now filter the repetitive "gene name/id ... is ambiguous" warnings from make_index(), and progress_bar=False is set on from_reference/add_sample_from_bam/add_qc_metrics/ add_orf_prediction in 03/03b to avoid multi-line tqdm spam in cached output. 02_api_vs_cli.ipynb's CLI calls filter the same warnings via grep -v.
New notebook 07_gene_model_characteristics.ipynb covers gene/transcript access, str_var_calculation/triangle_plot, entropy_calculation, and gene_track(colorbySqanti=True) -- previously uncovered by any tutorial.
Add importing SQANTI classification file function into 05_qc.ipynb.
Dependency Review✅ No vulnerabilities or license issues or OpenSSF Scorecard issues found.Scanned FilesNone |
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Summary
find_splice_bubbles.tridfilter bug (Using the demonstration_data, gives error: ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() #19), and other stale claims (.tbirequirement,tpm->cpmlabels).colorbySqanti), a QC metric distribution section, SQANTI3 classification import, and an expanded splicing coordination example.SQANTI_PALETTEextracted as a shared constant, GM12878/K562 coloring standardized across notebooks, Conclusion sections added, logo resized,quickstart.rstfixes.Test plan
black --checkandflake8clean