[Biopython] when is a SeqRecord not a SeqRecord

[Dilara Ally]

Hi

I'm trying to understand what is why when I print filtered_rec I get a
SeqRecord but if I try to access any particular attribute of a SeqRecord
such as letter_annotations I sometimes get an attribute error --
AttributeError: 'NoneType' object has no attribute 'letter_annotations.'


q_threshold=20

def check_meanQ(record, q_threshold):
    seqlen=len(record)
    quality_scores=array(record.letter_annotations["phred_quality"])
    if round(quality_scores.mean()) <= q_threshold:
        print "Discarded ", record.id, "because mean Q was",
round(quality_scores.mean())
    elif round(quality_scores.mean()) > q_threshold:
        return record

from Bio import SeqIO
for rec in SeqIO.parse("test.fastq", "fastq"):
    print rec.id
    filtered_rec= check_meanQ(rec, q_threshold)
    #print filtered_rec
    print filtered_rec.letter_annotations

I've attached two fastq files that I've used with this code one is called
test.fastq and the other is hiseq_pe_test.fastq

Any help would be greatly appreciated.
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