Tuesday, April 30, 2013

How to count nucleotide sequences from a fasta file #python

To count nucleotides in a Fasta file:

from Bio import SeqIO

for seq in SeqIO.parse('chrA01.fasta', 'fasta'):
    s = str(seq.seq)
    print s.count('T') + s.count('G') + s.count('C') + s.count('A')

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from Bio import SeqIO

for seq in SeqIO.parse('chrA01.fasta', 'fasta'):
    print s.count('T') + s.count('G') + s.count('C') + s.count('A') + s.count('N')

-------------------------------------------------------
from Bio import SeqIO

for seq in SeqIO.parse('chrA01.fasta', 'fasta'):
    print len(seq.seq)

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