MAF To Variant Classification Example¶

This notebook tests the read_maf method from the pyMut.input module that generates a PyMutation object. The read_maf function now includes automatic caching functionality for improved performance.

In [1]:

# Path to MAF file
maf_path = "../../../src/pyMut/data/examples/MAF/tcga_laml.maf.gz"
print(f'📂 Loading file: {maf_path}')

# Path to MAF file maf_path = "../../../src/pyMut/data/examples/MAF/tcga_laml.maf.gz" print(f'📂 Loading file: {maf_path}')

📂 Cargando archivo: ../../../src/pyMut/data/examples/MAF/tcga_laml.maf.gz

In [2]:

from pyMut.input import read_maf
import time

# Read the MAF file and generate the PyMutation object
print("First read (will create cache)...")
start_time = time.time()
py_mutation = read_maf(maf_path, assembly="37")
first_read_time = time.time() - start_time
print(f"First read completed in {first_read_time:.3f} seconds")

# Show the resulting object
print(py_mutation)

from pyMut.input import read_maf import time # Read the MAF file and generate the PyMutation object print("First read (will create cache)...") start_time = time.time() py_mutation = read_maf(maf_path, assembly="37") first_read_time = time.time() - start_time print(f"First read completed in {first_read_time:.3f} seconds") # Show the resulting object print(py_mutation)

2025-08-01 00:57:10,611 | INFO | pyMut.input | Starting MAF reading: ../../../src/pyMut/data/examples/MAF/tcga_laml.maf.gz
2025-08-01 00:57:10,611 | INFO | pyMut.input | Loading from cache: ../../../src/pyMut/data/examples/MAF/.pymut_cache/tcga_laml.maf_8bfbda65c4b23428.parquet

Primera lectura (creará cache)...

2025-08-01 00:57:10,651 | INFO | pyMut.input | Cache loaded successfully in 0.04 seconds

Primera lectura completada en 0.041 segundos
<pyMut.core.PyMutation object at 0x7c46f70df280>

In [3]:

py_mutation.configure_high_quality_plots()

py_mutation.variant_classification_plot()

py_mutation.configure_high_quality_plots() py_mutation.variant_classification_plot()

Out[3]:

In [4]:

# py_mutation.configure_high_quality_plots()
py_mutation.summary_plot()

# py_mutation.configure_high_quality_plots() py_mutation.summary_plot()

Out[4]:

In [5]:

# py_mutation.configure_high_quality_plots()
py_mutation.variant_type_plot()

# py_mutation.configure_high_quality_plots() py_mutation.variant_type_plot()

Out[5]: