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

[Brian Osborne]

Marc,

An example input file for Bio::CodonUsage::IO is t/data/MmCT.

Brian O.


On 4/21/06 9:26 AM, "Marc Logghe" <Marc.Logghe at DEVGEN.com> wrote:

> Hi Brian
> Thanks for the reply.
> I might be overlooking something but I dowloaded this last week. The
> tarball contained *.codon and *.spsum files and did not look at all like
> as a codon usage table (kind of pseudo fasta). For that reason, I used
> EMBOSS cutgextract that produced *.cut files starting from the CUTG
> *.codon files. 
> 
> I finally managed to parse this *.cut files.
> In order to do that I created a Bio::CodonUsage::IO::emboss module that
> only contains the private _parse() method. The setup I used is a copycat
> from Bio::SeqIO.
> Meaning, now you can do:
> my $io  = Bio::CodonUsage::IO->new( -file => shift, -format => 'emboss'
> );
> 
> In case no format option is given it defaults to the
> Bio::CodonUsage::IO::default module that contains the _parse() method
> from the original Bio::CodonUsage::IO module. Actually, this should be
> changed to a name that makes more sense but I did not know what this
> default format looks like and/or where it comes from. My guess it is
> coming from http://www.kazusa.or.jp but the site seems to be broken. At
> least today.
> Currently I continue with this setup in house, but in case you think it
> is usefull to commit, just let me know.
> Cheers,
> Marc
> 
>  
> 
>> -----Original Message-----
>> From: Brian Osborne [mailto:osborne1 at optonline.net]
>> Sent: Friday, April 21, 2006 3:09 PM
>> To: Marc Logghe; bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] Input for Bio::CodonUsage::IO
>> 
>> 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
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> 
> 
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