Adding --phylipout to MAFFT wrapper

biopython · Jul 8, 2013 · d03302c · d03302c
1 parent 3342be9
commit d03302c
Showing 1 changed file with 14 additions and 7 deletions.
diff --git a/Bio/Align/Applications/_Mafft.py b/Bio/Align/Applications/_Mafft.py
@@ -286,19 +286,26 @@ def __init__(self, cmd="mafft", **kwargs):
             _Switch(["--fmodel", "fmodel"],
                     "Incorporate the AA/nuc composition information into "
                     "the scoring matrix (True) or not (False, default)"),
-            #Name length n in a CLUSTAL format output can be controlled by --
-            #clustalout --namelength n.
-            #Support for titles of >10 characters in the phylip format (--
-            #phylipout --namelength n).  n = 10 by default.
+            #**** Output ****
+            #Name length for CLUSTAL and PHYLIP format output
             _Option(["--namelength", "namelength"],
-                    "Name length n in a CLUSTAL format output can be controlled "
-                    "by --clustalout --namelength n.",
+                    """Name length in CLUSTAL and PHYLIP output.
+
+                    MAFFT v6.847 (2011) added --namelength for use with
+                    the --clustalout option for CLUSTAL output.
+
+                    MAFFT v7.024 (2013) added support for this with the
+                    --phylipout option for PHYLIP output (default 10).
+                    """,
                     checker_function=lambda x: isinstance(x, int),
                     equate=False),
-            #**** Output ****
             #Output format: clustal format. Default: off (fasta format)
             _Switch(["--clustalout", "clustalout"],
                     "Output format: clustal (True) or fasta (False, default)"),
+            #Output format: phylip format.
+            #Added in beta with v6.847, fixed in v6.850 (2011)
+            _Switch(["--phylipout", "phylipout"],
+                    "Output format: phylip (True), or fasta (False, default)"),
             #Output order: same as input. Default: on
             _Switch(["--inputorder", "inputorder"],
                     "Output order: same as input (True, default) or alignment "