Simple script to calculate base percentages from a BAM file.

base_percentages_from_bam.py

import pysam
import argparse
from collections import Counter

def get_args():
    """Parse sys.argv"""
    parser = argparse.ArgumentParser()

    parser.add_argument('--bam',
                        required=True,
                        help='Path to BAM file.')

    parser.add_argument('output',
                        type=argparse.FileType('w'),
                        help="Path to BAM file. Default is STOUT")

    args = parser.parse_args()
    return args

args = get_args()
samfile = pysam.Samfile( args.bam, "rb" )
iter = samfile.pileup()

header = ['chrm', 'pos', 'A-count','C-count','T-count','G-count', 'A-proportion','C-proportion','T-proportion','G-proportion']

args.output.write('\t'.join(header) + "\n")

for c, p in enumerate(iter):

    bases = [pileupread.alignment.seq[pileupread.qpos] for pileupread in p.pileups]
    base_counts = Counter(bases)
    total = float(sum(base_counts.values()))

    final_line = [ samfile.getrname(p.pileups[0].alignment.rname), p.pos]

    final_line.extend( [base_counts[b] for b in ('A','C','T','G')] )
    final_line.extend( ["{0:.2f}".format(round(base_counts[b]/total,2)) for b in ('A','C','T','G')] )

    final_formated_line =  '\t'.join(map(str, final_line))
    args.output.write(final_formated_line + "\n")