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

Marc Logghe Marc.Logghe at DEVGEN.com
Fri Apr 21 04:56:02 EDT 2006

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
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 ?

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