[Bioperl-l] Script taxonomy2tree version 1.4 crashed on 110 species

Sendu Bala bix at sendu.me.uk
Sat Dec 16 09:47:57 EST 2006


Gabriel Valiente wrote:
>> I don't think that can be true. Your error message contains 'Must supply
>> a Bio::Taxon'. Bio::Taxon only exists in 1.5.2 (or cvs live).
>>
>> If you uninstall the fink installation and install 1.5.2 using cpan 
>> (with root privileges by going sudo cpan) that should at least get rid 
>> of the error messages...
>>
>>
>>> The tree is not correct (I've parsed it from R to have a double
>>> check) but don't know yet what the problem is with it.
>>
>> ... But if the tree is wrong anyway... Let me know what you find out.
> 
> I've uninstalled the fink installation and used the cvs instead, and the 
> error message is gone. However, on a larger set of 190 species, which 
> are all present in the NCBI taxonomy, the resulting tree has only 178 
> taxa. I suspect, something must be wrong with the merge_lineage method 
> in the major rewrite of the taxonomy2tree script. Can someone please 
> check this? I'm attaching the 190 species call to the script. Thanks,

Ok, I'll look into it. You're also welcome to see if you can take your 
own code from your original taxonomy2tree script and see if you can 
merge/replace the appropriate Bio::Tree::TreeFunctionsI methods with 
your algorithms to get it working correctly. Indeed, does your original 
version of the script work on this data set?


Cheers,
Sendu.


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