From d03302cc8d50ef1d148cb377b36c0f7fc84c1d46 Mon Sep 17 00:00:00 2001 From: peterjc Date: Mon, 8 Jul 2013 14:31:13 +0100 Subject: [PATCH] Adding --phylipout to MAFFT wrapper --- Bio/Align/Applications/_Mafft.py | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/Bio/Align/Applications/_Mafft.py b/Bio/Align/Applications/_Mafft.py index 5ae1d54c6ff..c33480ae05c 100644 --- 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 "