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google-code-export / phyutility

Automatically exported from code.google.com/p/phyutility
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doesn't put quotes around taxon names with special characters #8

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. run phyutility on a newick file containing a taxon name with a dash
2. execute tree file in paup (alignment file contains single quotes around that 
taxon)
3. ERROR!  

What is the expected output? What do you see instead?
Phyutility should check for the list of characters not recognized by macclade 
or paup and put 
single quotes around those taxa.  Other scripts check for this, including 
seqConverger.pl, which 
unfortunately doesn't convert tree files.

What version of the product are you using? On what operating system?
v.2.2.1
Mac OS 10.6

Please provide any additional information below.
it would be great to have this extra conversion step included in the next 
version.  Thanks for an 
otherwise great program!

Original issue reported on code.google.com by reti...@gmail.com on 10 Dec 2009 at 7:48

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GoogleCodeExporter commented 9 years ago 
I am thinking of having a flag for this to turn it on. For example, quotes may 
not be
recognized in other programs causing problems there. Nevertheless, looking into 
it.

Original comment by blackrim on 8 Apr 2010 at 2:49