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#!/usr/bin/env python
"""Write out a FASTA file.
Writing is more complicated and requires a few things from Bio.
Biopython's writing method expects to be given a list of SeqRecord objects and
it will write them to a file. Each SeqRecord object contains a Seq object that
has the actual sequence (and what type of sequence it is) as well as an id.
"""
try:
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_rna
except ImportError:
print "Sorry, you need Biopython to run this."
import sys
sys.exit(1)
sequences = [
"ACGGCG",
"ACGCGT",
"CCCCGC",
]
list_to_write = list()
count = 1
for sequence in sequences:
# since we are writing RNA, replace T with U (though Bio doesn't care)
sequence = sequence.replace("T", "U")
new_sequence = SeqRecord(Seq(sequence, generic_rna), id=str(count))
list_to_write.append(new_sequence)
count += 1
with open("my_first_fasta.fasta", "wb") as f:
SeqIO.write(list_to_write, f, "fasta")