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Fix the option used for ClustalOmega, when one wants to specify the

sequence type.  The previously used --t would be interpreted by
clustalo as a shortcut for --threads, resulting in error.
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1 parent a594cd8 commit 399bb64e3c38612170678a91861996c5860d2efd @cbrueffer cbrueffer committed with peterjc Nov 20, 2012
Showing with 1 addition and 1 deletion.
  1. +1 −1 Bio/Align/Applications/
2 Bio/Align/Applications/
@@ -63,7 +63,7 @@ def __init__(self, cmd="clustalo", **kwargs):
"Pre-aligned multiple sequence file (aligned columns will be kept fix).",
- _Option(["--t", "--seqtype", "seqtype"],
+ _Option(["-t", "--seqtype", "seqtype"],
"{Protein, RNA, DNA} Force a sequence type (default: auto).",
checker_function=lambda x: x in ["protein", "rna", "dna",

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