[Bioperl-l] TreeIO problem

[Dave Howorth]

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

<snip>
> 
> 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:
>>
>>(A,(B,C),(D,E))
>>
>>And it doesn't work either. 
>>
>>The original tree was:
>>
>>(Pf-CNP4:0.07786,(((Tr-CNP3:1.04017,Hs-CNP:0.90128):0.58396,
>>((((Tr-CNP1:0.20253,(Pf-CNP1:0.15012,(Om-CNP:0.12547,
>>Ol-CNP1:0.25526):0.03512):0.08989):0.14887,Omy-CNP1:0.36290):0.47164,
>>(Ol-CNP2:0.39033,Tr-CNP2:0.31133):0.71930):0.19555,
>>(Tr-BNP:0.20983,(Pf-BNP:0.15777,Om-BNP:0.17203):0.09696):0.98657):0.372
>>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