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Adding --phylipout to MAFFT wrapper

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commit d03302cc8d50ef1d148cb377b36c0f7fc84c1d46 1 parent 3342be9
@peterjc peterjc authored
Showing with 14 additions and 7 deletions.
  1. +14 −7 Bio/Align/Applications/_Mafft.py
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21 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 "
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