Reading MAF Files with pyMut¶

This notebook demonstrates how to read MAF files using the read_maf method from pyMut.

Example: Loading TCGA LAML MAF file¶

We'll load the tcga_laml.maf.gz file using assembly 37.

In [1]:

# Import the read_maf function
from pyMut.input import read_maf

# Import the read_maf function from pyMut.input import read_maf

In [2]:

# Load the MAF file
maf_path = "../../../src/pyMut/data/examples/MAF/tcga_laml.maf.gz"
py_mut = read_maf(path=maf_path, assembly="37")

# Load the MAF file maf_path = "../../../src/pyMut/data/examples/MAF/tcga_laml.maf.gz" py_mut = read_maf(path=maf_path, assembly="37")

2025-08-01 01:44:49,103 | INFO | pyMut.input | Starting MAF reading: ../../../src/pyMut/data/examples/MAF/tcga_laml.maf.gz
2025-08-01 01:44:49,105 | INFO | pyMut.input | Loading from cache: ../../../src/pyMut/data/examples/MAF/.pymut_cache/tcga_laml.maf_8bfbda65c4b23428.parquet
2025-08-01 01:44:49,131 | INFO | pyMut.input | Cache loaded successfully in 0.03 seconds

In [3]:

# Display the first 5 rows
py_mut.head()

# Display the first 5 rows py_mut.head()

Out[3]:

	CHROM	POS	ID	REF	ALT	QUAL	FILTER	TCGA-AB-2988	TCGA-AB-2869	TCGA-AB-3009	...	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	Tumor_Sample_Barcode	Protein_Change	i_TumorVAF_WU	i_transcript_name
0	chr9	100077177	.	T	C	.	.	T|T	T|T	T|T	...	+	SILENT	SNP	T	T	C	TCGA-AB-2886	p.T431T	9.76	NM_020893.1
1	chr9	100085148	.	G	A	.	.	G|G	G|G	G|G	...	+	MISSENSE_MUTATION	SNP	G	G	A	TCGA-AB-2917	p.R581H	18.4	NM_020893.1
2	chr9	100971322	.	A	C	.	.	A|A	A|A	A|A	...	+	MISSENSE_MUTATION	SNP	A	A	C	TCGA-AB-2841	p.L593R	45.83	NM_018421.3
3	chr9	104086335	.	C	T	.	.	C|C	C|C	C|C	...	+	MISSENSE_MUTATION	SNP	C	C	T	TCGA-AB-2877	p.T325I	37.12	NM_017753.2
4	chr9	104124840	.	G	A	.	.	G|A	G|G	G|G	...	+	MISSENSE_MUTATION	SNP	G	G	A	TCGA-AB-2988	p.T376M	48.35	NM_001701.1

5 rows × 216 columns