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Fix to filter by mean, not minimum quality score #1

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Fix to filter by mean, not minimum quality score #1

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9 changes: 5 additions & 4 deletions short-read-assembly/filter_reads.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,12 +14,13 @@
rec1 = iter.next()
rec2 = iter.next()

rec1_bad_bases = [x for x in rec1.letter_annotations["phred_quality"] if x < THRESHOLD]
rec2_bad_bases = [x for x in rec2.letter_annotations["phred_quality"] if x < THRESHOLD]
rec_1_qualities = rec1.letter_annotations["phred_quality"]
rec_2_qualities = rec2.letter_annotations["phred_quality"]

rec1_bad_bases = sum(rec_1_qualities)/len(rec_1_qualities) < THRESHOLD
rec2_bad_bases = sum(rec_2_qualities)/len(rec_2_qualities) < THRESHOLD

if not rec1_bad_bases and not rec2_bad_bases:
SeqIO.write([rec1, rec2], sys.stdout, "fastq-illumina")
except StopIteration, e:
pass