[Biopython] MUSCLE for alignment

[Peter Cock]

On Sat, Apr 6, 2013 at 12:18 PM, 林行众 <linxzh1989 at gmail.com> wrote:
> Thank you! Peter.
> It really helps me.
> If i do not specify it by: stdout, stderr = mcline()
> the alignment will writen to stdout, instead of the output file.
> Is it correct?

MUSCLE will by default write the alignment to stdout, but you
used the out argument to specify an output filename instead.
In this case stdout will probably be empty.

There are some stdout examples using MUSCLE in the
Biopython Tutorial:
http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf

Peter

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