Percent Identity of reads from a BAM file

get_read_info.py

import pysam
bamfile = pysam.AlignmentFile('file.bam')

for read in bamfile.fetch():
    number_of_mismatches = read.get_tag("NM")
    read_length = read.infer_query_length()
    read_percent_id = (1 - float(number_of_mismatches) / float(read_length)) * 100
    
    # if you want a specific read
    if read.query_name == 'my_read':
        print(read_percent_id)