Module 11

Reading multiple records

Processing many sequences.

Many records

You can loop over SeqIO records just like you loop over a list. This lets you process many sequences at once.

from Bio import SeqIO
from io import StringIO
fasta = ">A\nATGC\n>B\nGGGG\n>C\nTTTT"
handle = StringIO(fasta)
count = 0
for record in SeqIO.parse(handle, "fasta"):
    count += 1
print(count, "records")
Your task

Count records

  • Count how many records are in a multi-FASTA.