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idolawoye/count_N_percentage.py

Created June 11, 2022 13:37
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Python script to count number of Ns in a multifasta file
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count_N_percentage.py
#!/usr/bin/env python
from Bio import SeqIO
fasta = "the_fasta_file.fasta"
for record in SeqIO.parse(fasta, "fasta"):
print("ID: %s" % record.id)
print("Sequence length: %s" % len(record))
print("Number of Ns: %s" % record.seq.count('N'))
print((record.seq.count('N')/len(record))*100)
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