Module 11

Reading FASTA

Parsing FASTA with SeqIO.

Easy FASTA parsing

SeqIO.parse() reads a FASTA file and yields SeqRecord objects. Each record has an id and a sequence.

from Bio import SeqIO
from io import StringIO
fasta_data = ">Tv01\nATGC\n>Tv02\nGGGG"
handle = StringIO(fasta_data)
for record in SeqIO.parse(handle, "fasta"):
    print(record.id, len(record))

Your task

Read FASTA with SeqIO

Parse a FASTA string and print each record's id and length.

11.10 · SeqIO 11.12 · Reading multiple records