[Bioperl-l] Input for Bio::CodonUsage::IO

Brian Osborne osborne1 at optonline.net
Fri Apr 21 09:09:12 EDT 2006


Marc,

It wants a file from the database CUTG. You can ftp them from this mirror:

ftp://ftp.ebi.ac.uk/pub/databases/cutg


Brian O.


On 4/21/06 4:56 AM, "Marc Logghe" <Marc.Logghe at DEVGEN.com> wrote:

> Hi,
> I was wondering what format Bio::CodonUsage::IO expects as input for the
> -file option.
> I tried to pass it a *.cut file generated by EMBOSS' cutgextract that
> looks like this:
> #Species: Oryza sativa
> #Division: gbpln
> #Release: CUTG
> #CdsCount: 70050
> 
> #Coding GC 55.34%
> #1st letter GC 58.41%
> #2nd letter GC 46.34%
> #3rd letter GC 61.29%
> 
> #Codon AA Fraction Frequency Number
> GCA    A     0.185    17.382 431151
> <skipped>
> TGA    *     0.435     1.228  30463
> 
> Looking into the _parse() method of Bio::CodonUsage::IO it appears that
> the table resembles this kind of format but is actually not exactly what
> it expects. My question is: how should it really look like ? I could not
> find an example in t/data.
> Any clues ?
> Thanks,
> Marc 
> 
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