MuscleCommandline example using stdin and stdout broken on Python 3 about biopython HOT 6 CLOSED

How are you creating the child process with subprocess, and in particular did you ask for unicode rather than bytes in the stdin/stdout/stderr handles by using the (oddly named) universal_newlines=True option?

[Update: You said wiki example but pointed at the tutorial, if the universal_newlines=True trick works would you like to prepare an update to Doc/Tutorial.tex adding it?]

We use this option in Bio.Applications so that the everything is a (unicode) string rather than bytes. This seemed best for most of the command line tools we wrap (one exception is binary formats like SFF or BAM).

from biopython.

The universal_newlines option did the trick. I probably would not have figured that out unless I reached the point of desperation, since the option name seems quite unrelated to the effect in this case.

Thanks.

from biopython.

I presume the thought process was that handling DOS/Windows vs Old Mac vs Unix newlines already required a handle wrapper, where file pointers via seek/tell are not transparent, and so that universal newlines code was co-opted during the bytes/unicode separation for Python 3. But is it a stupidly named argument :(

from biopython.

Tutorial example updated 522a693 - thanks for reporting this.

from biopython.

Sorry, I missed your edit about updating the tutorial. I would have been happy to update it!

from biopython.

With hindsight an extra comment would have been better than adding the note to the existing comment. Never mind.

from biopython.