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updated: cli parameters for Water and Needle wrappers

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1 parent e644950 commit f03bb45f1b79d3e0341ef8f13cc2a829c41b5c27 @bow bow committed with peterjc May 11, 2012
Showing with 15 additions and 0 deletions.
  1. +15 −0 Bio/Emboss/Applications.py
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@@ -785,6 +785,10 @@ def __init__(self, cmd="water", **kwargs):
_Option(["-datafile","datafile"],
"Matrix file",
filename=True),
+ _Switch(["-nobrief", "nobrief"],
+ "Display extended identity and similarity"),
+ _Switch(["-brief", "brief"],
+ "Display brief identity and similarity"),
_Option(["-similarity","similarity"],
"Display percent identity and similarity"),
_Option(["-snucleotide","snucleotide"],
@@ -818,6 +822,17 @@ def __init__(self, cmd="needle", **kwargs):
_Option(["-datafile","datafile"],
"Matrix file",
filename=True),
+ _Option(["-endweight", "endweight"],
+ "Apply And gap penalties"),
+ _Option(["-endopen", "endopen"],
+ "The score taken away when an end gap is created."),
+ _Option(["-endextend", "endextend"],
+ "The score added to the end gap penality for each base or "
+ "residue in the end gap."),
+ _Switch(["-nobrief", "nobrief"],
+ "Display extended identity and similarity"),
+ _Switch(["-brief", "brief"],
+ "Display brief identity and similarity"),
_Option(["-similarity","similarity"],
"Display percent identity and similarity"),
_Option(["-snucleotide","snucleotide"],

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