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import sys | |
# please install the following requirements: pandas, pysam, biopython | |
import pandas as pd | |
import pysam | |
from Bio import SeqIO | |
# python filter_reference_from_alignment.py input.bam references.fasta mapping_statistics.csv filtered_references.fasta | |
inputbam, inputref, outputcsv, outputfasta = sys.argv[1:] |