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Sync with ClustalW 2.1. This includes three commented out options tha…

…t appear

more than once in the ClustalW help.  They are added to make comparisons to the
-help output of a newer release easier.
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commit 9f1e197afa91b020351829722de15d562196adbb 1 parent aac3162
@cbrueffer cbrueffer authored peterjc committed
Showing with 26 additions and 9 deletions.
  1. +26 −9 Bio/Align/Applications/_Clustalw.py
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35 Bio/Align/Applications/_Clustalw.py
@@ -33,7 +33,7 @@ class ClustalwCommandline(AbstractCommandline):
Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0.
Bioinformatics, 23, 2947-2948.
- Last checked against versions: 1.83 and 2.0.10
+ Last checked against versions: 1.83 and 2.1
"""
#TODO - Should we default to cmd="clustalw2" now?
def __init__(self, cmd="clustalw", **kwargs):
@@ -61,6 +61,8 @@ def __init__(self, cmd="clustalw", **kwargs):
"Do full multiple alignment."),
_Switch(["-tree", "-TREE", "TREE", "tree"],
"Calculate NJ tree."),
+ _Switch(["-pim", "-PIM", "PIM", "pim"],
+ "Output percent identity matrix (while calculating the tree)."),
_Option(["-bootstrap", "-BOOTSTRAP", "BOOTSTRAP", "bootstrap"],
"Bootstrap a NJ tree (n= number of bootstraps; def. = 1000).",
checker_function=lambda x: isinstance(x, int)),
@@ -87,11 +89,11 @@ def __init__(self, cmd="clustalw", **kwargs):
"Output sequence alignment file name",
filename=True),
_Option(["-output", "-OUTPUT", "OUTPUT", "output"],
- "Output format: GCG, GDE, PHYLIP, PIR or NEXUS",
- checker_function=lambda x: x in ["GCG", "GDE", "PHYLIP",
- "PIR", "NEXUS",
- "gcg", "gde", "phylip",
- "pir", "nexus"]),
+ "Output format: CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTA",
+ checker_function=lambda x: x in ["CLUSTAL", "GCG", "GDE", "PHYLIP",
+ "PIR", "NEXUS", "FASTA",
+ "clustal", "gcg", "gde", "phylip",
+ "pir", "nexus", "fasta"]),
_Option(["-outorder", "-OUTORDER", "OUTORDER", "outorder"],
"Output taxon order: INPUT or ALIGNED",
checker_function=lambda x: x in ["INPUT", "input",
@@ -160,7 +162,7 @@ def __init__(self, cmd="clustalw", **kwargs):
checker_function=lambda x: isinstance(x, int) or \
isinstance(x, float)),
_Option(["-pwgapext", "-PWGAPEXT", "PWGAPEXT", "pwgapext"],
- "Gap opening penalty",
+ "Gap extension penalty",
checker_function=lambda x: isinstance(x, int) or \
isinstance(x, float)),
# ***Multiple Alignments:***
@@ -209,6 +211,12 @@ def __init__(self, cmd="clustalw", **kwargs):
"% ident. for delay",
checker_function=lambda x: isinstance(x, int) or \
isinstance(x, float)),
+ # Already handled in General Settings section, but appears a second
+ # time under Multiple Alignments in the help
+ #_Option(["-type", "-TYPE", "TYPE", "type"],
+ # "PROTEIN or DNA",
+ # checker_function=lambda x: x in ["PROTEIN", "DNA",
+ # "protein", "dna"]),
_Option(["-transweight", "-TRANSWEIGHT", "TRANSWEIGHT", "transweight"],
"Transitions weighting",
checker_function=lambda x: isinstance(x, int) or \
@@ -244,11 +252,20 @@ def __init__(self, cmd="clustalw", **kwargs):
# ***Sequence to Profile Alignments:***
_Switch(["-sequences", "-SEQUENCES", "SEQUENCES", "sequences"],
"Sequentially add profile2 sequences to profile1 alignment"),
+ # These are already handled in the Multiple Alignments section,
+ # but appear a second time here in the help.
+ #_Option(["-newtree", "-NEWTREE", "NEWTREE", "newtree"],
+ # "File for new guide tree",
+ # filename=True),
+ #_Option(["-usetree", "-USETREE", "USETREE", "usetree"],
+ # "File for old guide tree",
+ # checker_function=lambda x: os.path.exists,
+ # filename=True),
+ # ***Structure Alignments:***
_Switch(["-nosecstr1", "-NOSECSTR1", "NOSECSTR1", "nosecstr1"],
"Do not use secondary structure-gap penalty mask for profile 1"),
_Switch(["-nosecstr2", "-NOSECSTR2", "NOSECSTR2", "nosecstr2"],
"Do not use secondary structure-gap penalty mask for profile 2"),
- # ***Structure Alignments:***
_Option(["-secstrout", "-SECSTROUT", "SECSTROUT", "secstrout"],
"STRUCTURE or MASK or BOTH or NONE output in alignment file",
checker_function=lambda x: x in ["STRUCTURE", "MASK",
@@ -281,7 +298,7 @@ def __init__(self, cmd="clustalw", **kwargs):
"Number of residues inside strand to be treated as terminal",
checker_function=lambda x: isinstance(x, int)),
_Option(["-strandendout", "-STRANDENDOUT", "STRANDENDOUT", "strandendout"],
- "number of residues outside strand to be treated as terminal",
+ "Number of residues outside strand to be treated as terminal",
checker_function=lambda x: isinstance(x, int)),
# ***Trees:***
_Option(["-outputtree", "-OUTPUTTREE", "OUTPUTTREE", "outputtree"],
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