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Remove remnants of ClustalW.

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commit 314a870e7a6edc0947832954b8efd225ff3b4e31 1 parent ff5865e
@cbrueffer cbrueffer authored peterjc committed
Showing with 3 additions and 4 deletions.
  1. +3 −4 Tests/test_ClustalOmega_tool.py
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7 Tests/test_ClustalOmega_tool.py
@@ -114,12 +114,12 @@
(temp_filename_with_spaces, "temp with space.aln", None),
(temp_large_fasta_file, "temp_cw_prot.aln", None),
]:
- #Note that ClustalW will map ":" to "_" in it's output file
+ #Note that ClustalOmega will map ":" to "_" in it's output file
input_records = SeqIO.to_dict(SeqIO.parse(input_file,"fasta"),
lambda rec : rec.id.replace(":","_"))
if os.path.isfile(output_file):
os.remove(output_file)
- print "Calling clustalw on %s (with %i records)" \
+ print "Calling clustalo on %s (with %i records)" \
% (repr(input_file), len(input_records))
print "using output file %s" % repr(output_file)
if newtree_file is not None:
@@ -146,8 +146,7 @@
error.startswith("WARNING: DNA alignment is still experimental."), error
#Check the output...
align = AlignIO.read(output_file, "clustal")
- #The length of the alignment will depend on the version of clustalw
- #(clustalw 2.0.10 and clustalw 1.83 are certainly different).
+ #The length of the alignment will depend on the version of clustalo
print "Got an alignment, %i sequences" % (len(align))
output_records = SeqIO.to_dict(SeqIO.parse(output_file,"clustal"))
assert len(set(input_records.keys())) == len(set(output_records.keys())), \
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