bbglab/oncodrive3d: Release v1.0.9

Le résumé fourni par la source

Oncodrive3D v1.0.9 New features Docker & Singularity support: published container image variants on Docker Hub (base, ChimeraX, and full variants) bundling ChimeraX and PDB_Tool, with a docker.sh build/push script, updated Nextflow pipeline module references, and instructions for obtaining chimerax.deb. README now documents Singularity path-binding requirements (#102). Custom ΔΔG predictions: build datasets now accept user-supplied ΔΔG inputs, with WT-sequence validation, deduplication, a configurable mismatch threshold, and improved skip-reason reporting (#90, #91). ChimeraX plotting: mutated residues are now rendered as spheres for better visibility, with optimized handling of mutated positions by reusing computed values (#107). AlphaFold version auto-detection in chimerax-plot (read from the data directory) (#103). Helper script get_regions_file for computing genome size and generating the regions file (#93). Performance Parallel PDB_Tool: feature extraction now runs across multiple processes for a significant speed-up on large datasets (#98). Vectorized ΔΔG parsing: CSV ingestion rewritten with vectorized operations and a compiled variant regex; removed unused helpers (#92). Skip ΔΔG input copy: build_annotations now reads user-supplied ΔΔG directories directly instead of copying them (#95, #96). Capped download concurrency (max 4 threads) to avoid rate-limit/throughput issues (#88). Bug fixes Handle infinite values in the anomaly score computation (#100). Fix ordering bug in mutability-status reporting: genes_not_mutability was computed from the already-filtered genes_to_process list, so it was always empty (and triggered a downstream UnboundLocalError). Also use per-gene values for Mut_in_gene (#101). ChimeraX path safety: paths inside ChimeraX --cmd scripts are now quoted and validated to handle spaces and prevent unsafe-character injection (#106). ChimeraX/plot robustness: subprocess invocations use argv lists, handle OSError and non-zero exit codes, redirect stdout, and capture stderr; score capping no longer overflows on +inf values (#105). Singularity HOME redirection: redirect HOME to /tmp so ChimeraX can write its data directory under Singularity (#103, #104). Opt in to regex=True in uniprot_feat to silence the pandas str.replace deprecation warning (#99). Restrict ΔΔG fragment glob to .csv files to avoid picking up sibling files (#94). Skip the ΔΔG step for Mus musculus when ddg_dir is missing, and avoid downloading the human ΔΔG bundle on mouse builds (#89). Update default AlphaFold version in CLI options to 6. Improved error handling and logging in PDB_Tool and parse_ddg_rasp_worker (#94, #98). Documentation Major README restructuring: tables for output fields, clearer input requirements, container image usage, dataset-building and citation notes, AlphaFold versioning behavior (#93, #97). Build datasets and annotations docs: clarified ΔΔG defaults, --ddg_dir behavior, PDB_Tool installation, supplementary outputs, and MANE mapping details (#93). Full Changelog: https://github.com/bbglab/oncodrive3d/compare/v1.0.8...v1.0.9

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