Fixes for Muscle v5

rrwick · Oct 11, 2022 · 886fdd5 · 886fdd5
1 parent 399d7d4
commit 886fdd5
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/trycycler/msa.py b/trycycler/msa.py
@@ -111,7 +111,8 @@ def run_muscle_one_piece(parameters):
     if muscle_version.startswith('3'):
         muscle_command = ['muscle', '-in', input_filename, '-out', output_filename]
     elif muscle_version.startswith('5'):
-        muscle_command = ['muscle', '-align', input_filename, '-output', output_filename]
+        muscle_command = ['muscle', '-align', input_filename, '-output', output_filename,
+                          '-threads', '1']
     else:
         assert False
     with open(muscle_output_filename, 'wt') as muscle_output:

diff --git a/trycycler/software.py b/trycycler/software.py
@@ -78,6 +78,7 @@ def parse_muscle_version(output):
     elif 'muscle ' in output:  # For version 5
         output = output.split('muscle ')[1]
         output = output.split('_')[0]
+        output = output.split('\n')[0]
         return output.strip()
     else:
         return '?'