[Biopython-dev] skipping a bad record in SeqIO.parse

[Iddo Friedberg]

Suppose SeqIO throws an exception due to a bad record. I want to note that
in stderr an move on to the next record. How do i do that?


The following eyesore of a code simply leaves me stuck reading the same bad
record over and over:

   seq_reader = SeqIO.parse(in_handle, format)
    while True:
        try:
            seq_record = seq_reader.next()
        except StopIteration:
            break
        except:
            if debug:
                sys.stderr.write("Sequence not read: %s%s" % (seq_record.id,
os.linesep))
                sys.stderr.flush()
            continue
        if not seq_record:
            break





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Iddo Friedberg, Ph.D.
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