pysam_bam_file_read_iteration_alignment_info_extraction.py

1import pysam
2
3# Open a BAM file for reading
4samfile = pysam.AlignmentFile("ex1.bam", "rb")
5
6# Iterate over the reads in the file
7for read in samfile:
8    # Print basic alignment information
9    print(f"Read name: {read.query_name}")
10    print(f"Reference ID: {read.reference_id}")
11    print(f"Reference Start: {read.reference_start}")
12    print(f"CIGAR: {read.cigarstring}")
13    print(f"Sequence: {read.query_sequence}")
14    print("-" * 20)
15
16# Close the file
17samfile.close()