pyMut 🧬¶
A Python library for gene mutation analysis and visualisation
🎯 Comparison with Other Tools¶
| FUNCTIONAL CRITERIA | PYMUT (PROPOSAL) | MUTSCAPE | MAFTOOLS |
|---|---|---|---|
| Input formats | VCF & MAF (native) | MAF | MAF |
| VEP annotation | ✓ | ||
| Genomic range filtering | ✓ | ✓ | ✓ |
| PASS category variant filtering | ✓ | ✓ | |
| Sample filtering | ✓ | ✓ | |
| Tissue expression filtering | ✓ | ✓ | |
| File format transformation | ✓ | ✓ (VCF to MAF only) | ✓ (VCF to MAF only) |
| File output | ✓ | ||
| File combination | ✓ | ✓ | |
| Significantly mutated genes (SMG) detection | ✓ | ||
| Cancer-related gene annotation | ✓ | ✓ | |
| Tumor mutational burden (TMB) calculation | ✓ | ✓ | |
| Mutational signature identification | ✓ | ||
| Medical implications mutation annotation | ✓ | ✓ | |
| PFAM annotation support | ✓ | ✓ | |
| Summary Plot | ✓ | ✓ | |
| Oncoplot | ✓ | ✓ | |
| Lollipop Plot | ✓ | ✓ | |
| Somatic Interactions Plot | ✓ | ✓ | |
| Mutational Signature Analysis | ✓ | ✓ | |
| CoMut Plot | ✓ | ✓ |
📋 Requirements¶
| Librería | Dependencias inmediatas |
|---|---|
| duckdb 1.3.2 | – Ninguna |
| fastparquet 2024.11.0 | – cramjam ≥ 2.3 – fsspec – numpy – packaging – pandas ≥ 1.5.0 |
| matplotlib 3.10.3 | – contourpy ≥ 1.0.1 – cycler ≥ 0.10 – fonttools ≥ 4.22.0 – kiwisolver ≥ 1.3.1 – numpy ≥ 1.23 – packaging ≥ 20.0 – pillow ≥ 8 – pyparsing ≥ 2.3.1 – python-dateutil ≥ 2.7 |
| mkdocs 1.6.1 | – click ≥ 7.0 – colorama ≥ 0.4 – ghp-import ≥ 1.0 – jinja2 ≥ 2.11.1 – markdown ≥ 3.3.6 – markupsafe ≥ 2.0.1 – mergedeep ≥ 1.3.4 – mkdocs-get-deps ≥ 0.2.0 – packaging ≥ 20.5 – pathspec ≥ 0.11.1 – pyyaml ≥ 5.1 – pyyaml-env-tag ≥ 0.1 – watchdog ≥ 2.0 |
| numpy 1.26.4 | – Ninguna |
| pandas 2.3.1 | – numpy ≥ 1.22.4 – python-dateutil ≥ 2.8.2 – pytz ≥ 2020.1 – tzdata ≥ 2022.7 |
| pyarrow 14.0.2 | – numpy ≥ 1.16.6 |
| pyensembl 2.3.13 | – datacache ≥ 1.4.0,<2.0.0 – gtfparse ≥ 2.5.0,<3.0.0 – memoized-property ≥ 1.0.2 – pylint ≥ 2.17.2,<3.0.0 – serializable ≥ 0.2.1,<1.0.0 – tinytimer ≥ 0.0.0,<1.0.0 – typechecks ≥ 0.0.2,<1.0.0 |
| pyfaidx 0.8.1.4 | – packaging |
| requests 2.32.4 | – certifi ≥ 2017.4.17 – charset-normalizer ≥ 2,<4 – idna ≥ 2.5,<4 – urllib3 ≥ 1.21.1,<3 |
| scikit-learn 1.7.1 | – joblib ≥ 1.2.0 – numpy ≥ 1.22.0 – scipy ≥ 1.8.0 – threadpoolctl ≥ 3.1.0 |
| scipy 1.11. 4 | – numpy ≥ 1.21.6,<1.28.0 |
| seaborn 0.13.2 | – matplotlib ≥ 3.4,<3.6.1 or >3.6.1 – numpy ≥ 1.20,<1.24.0 or >1.24.0 – pandas ≥ 1.2 |
| urllib3 2.5.0 | – Ninguna |
📄 License¶
This project is licensed under the MIT License - see the LICENSE file for details.