[Bioperl-l] TreeIO problem

Dave Howorth dhoworth at mrc-lmb.cam.ac.uk
Fri Apr 16 06:16:02 EDT 2004

Allen Day wrote:
> there is a problem with your newick input, or its interaction with the 
> TreeIO subsystem.  from the bioperl cvs, this code works:

The most obvious difference is that there is no semicolon at the end of 
both of Mikel's examples.  That's an error and I believe that will be 
enough to stop it working.

Cheers, Dave

> however using the newick data you provide below, the while loop is never 
> entered.  here is the data i am using from the bioperl regression tests.
> (
> CATH_RAT:0.31356,
> (
> CATL_HUMAN:0.13938,
> CATL_RAT:0.12788)
> :0.18794,
> PAPA_CARPA:0.34410);
> -Allen
> On Thu, 15 Apr 2004, Mikel Ega wrote:
>>At the end I have produced a Dummy simple tree to see if distances
>>affected in anything:
>>And it doesn't work either. 
>>The original tree was:
>>19):0.64073, Ol-CNP4:0.18286):0.10371,Tr-CNP4:0.09927)

Dave Howorth
MRC Centre for Protein Engineering
Hills Road, Cambridge, CB2 2QH
01223 252960

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