Description: raise runtime error when trying to use wrapper on muscle 5.
 The muscle wrapper only supports muscle 3, and the biopython project is aiming
 to remove wrapper support in an upcoming version.  Port of the wrapping code
 to support both muscle versions will thus probably never happen.  The affected
 code section is due to disappear in an upcoming biopython version and it thus
 not forwarded upstream.
Author: Étienne Mollier <emollier@debian.org>
Bug: https://github.com/biopython/biopython/issues/3902
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1009118
Last-Update: 2022-11-24
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- python-biopython.orig/Bio/Align/Applications/_Muscle.py
+++ python-biopython/Bio/Align/Applications/_Muscle.py
@@ -8,6 +8,7 @@
 
 
 from Bio.Application import _Option, _Switch, AbstractCommandline
+from subprocess import getoutput
 
 
 class MuscleCommandline(AbstractCommandline):
@@ -676,6 +677,10 @@
             #                           stdout and exit
             _Switch(["-version", "version"], "Write version string to stdout and exit"),
         ]
+        output = getoutput(cmd + " -version")
+        if "muscle 5" in output:
+            raise RuntimeError("muscle 5 is unsupported in biopython")
+
         AbstractCommandline.__init__(self, cmd, **kwargs)