[Biopython-dev] BWA Wrapper

[Peter Cock]

On Thu, Feb 14, 2013 at 7:43 PM, Lenna Peterson <arklenna at gmail.com> wrote:
>
> What's wrong with accepting the stdout string that the current
> implementation provides and explicitly writing it to your file?
>

That is only a good idea for short output, say up to a few kb.

With bwa (and samtools etc), quite often the output defaults
to (or only goes to) stdout - and can be very large. It can also
be binary rather than text, which is an additional complication
with Python 2 vs Python 3 (byte strings versus unicode strings).

See http://bio-bwa.sourceforge.net/bwa.shtml

Peter