Hello!
I have wrote this code in Python:
from Bio import SeqIO
fasta_file="OXA_finds.fasta"
output=open(fasta_file,'w')
gb_file="OXA_test.gb"
wanted=["Beta-lactamase class D"]
for record in SeqIO.parse(open(gb_file,"r"),"genbank"):
print("Name %s, %i features" % (record.name,len(record.features)))
print(repr(record.seq))
for f in record.features:
if f.type=="CDS" and "product" in f.qualifiers:
product=f.qualifiers["product"][0]
if product in wanted:
output.write(">%s,%s from %s\n%s\n" % (f.qualifiers['product'][0],f.qualifiers['locus_tag'][0],record.name,f.extract(record.seq)))
output.close()
So this code gives me a lot 'N' in FASTA file, and I want a dna string here. How can I handle that?
Thanks in advance!
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written
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fiascox12 •
The Ns are not a problem, you often find Ns in sequences. N corresponds to any nucleotide (not a gap). It means they didn't succeed to determine the base during the sequencing at this position.
If you prefer, adding a "if" statement, you can choose to avoid to work with sequences containing any N. I think is not a good idea because even with the presence of N, as they succeeded to determine that the sequence has "Beta-lactamase class D" as product, it means there is enough information in the sequence for determining the function (domains, orthology, etc ...).
I have already know what dna sequence I exactly needed. I need to copy sequence from http://www.ncbi.nlm.nih.gov/
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written
by
fiascox12 •
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Hello fiascox12!
It appears that your post has been cross-posted to another site: http://stackoverflow.com/questions/30344503
This is typically not recommended as it runs the risk of annoying people in both communities.