[Biopython] When is a SeqRecord a SeqRecord
Dilara Ally
dilara.ally at gmail.com
Tue Jul 17 22:24:07 UTC 2012
Hi
I've modified my code but why does the inclusion of return None and the
subsequent code if filtered_rec is not None solve the problem? Thanks!
Dilara
q_threshold=20
def check_meanQ(rec, q_threshold):
seqlen=len(rec)
quality_scores=array(rec.letter_annotations["phred_quality"])
if round(quality_scores.mean()) <= q_threshold:
print "Discarded ", rec.id, "because mean Q was",
round(quality_scores.mean())
return None
if round(quality_scores.mean()) > q_threshold:
return rec
from Bio import SeqIO
for rec in SeqIO.parse("test.fastq", "fastq"):
#print rec.id
filtered_rec= check_meanQ(rec, q_threshold)
if filtered_rec is not None:
print filtered_rec.id
print filtered_rec.letter_annotations
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