[Bioperl-l] What file format does Bio::CodonUsage::IO expect?

Chris Fields cjfields at uiuc.edu
Sun Apr 29 17:50:15 EDT 2007


Odd, when I run 'perl -I. t/DBCUTG.t' from CVS it works fine.  Of  
course, I am assuming that you are running the latest release (1.5.2).

Could you post a bug report with a script that generates the error?

chris

On Apr 29, 2007, at 9:06 AM, Ben McIlwain wrote:

> Chris Fields wrote:
>> One example file (MmCT) can be found in the test data directory in  
>> the
>> bioperl distribution (t/data directory) and some tests relevant to  
>> codon
>> table usage are found in DBCUTG.t.
>
> I still get the same warning message even when running on the given  
> test
> data?  That doesn't sound right.
>
> -------------------- WARNING ---------------------
> MSG: probable parsing error - should be 21 entries for 20aa + stop  
> codon
> ---------------------------------------------------
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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