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

Chris Fields cjfields at uiuc.edu
Sun Apr 29 10:05:59 EDT 2007


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.

chris

On Apr 29, 2007, at 8:43 AM, Ben McIlwain wrote:

> I'm trying to load up a table of codon usage frequencies I've  
> downloaded
> from the web using Bio::CodonUsage::IO.  My code looks like this:
>
>     use Bio::CodonUsage::Table;
>     use Bio::CodonUsage::IO;
>     # ...
>     my $io = Bio::CodonUsage::IO->new(-file=>$freqFile);
>     my $codonTable = $io->next_data();
>
> Unfortunately, I can't seem to find any documentation on what  
> format the
> codon usage table file is expected to be in, and all of my best  
> guesses
> seem to be invalid, yielding the following error message:
>
> -------------------- WARNING ---------------------
> MSG: probable parsing error - should be 21 entries for 20aa + stop  
> codon
> ---------------------------------------------------
>
> I've tried using both formats that are available from the Codon Usage
> Database (easily the largest source of codon usage frequencies),
> available here: http://www.kazusa.or.jp/codon/
>
> The two formats I've tried and failed look like this:
>
> UUU 32.5( 45732)  UCU 15.3( 21588)  UAU 27.8( 39146)  UGU  6.3(  8796)
> UUC 14.3( 20101)  UCC  3.2(  4458)  UAC  9.3( 13016)  UGC  2.1(  2971)
> ...
>
>
> AND
>
> AmAcid  Codon      Number    /1000     Fraction   ..
>
> Gly     GGG     13198.00      9.38      0.14
> Gly     GGA     34123.00     24.26      0.36
> ...
>
>
> So, anyone know how to get this downloaded codon usage data loaded up
> into a Bio::CodonUsage::Table object?  Bio::CodonUsage::IO doesn't  
> seem
> to like parsing the standard formats.  Thanks.
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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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