[Bioperl-l] OX lines of EMBL files [patch included]

Chris Fields cjfields at illinois.edu
Wed Dec 22 22:05:24 EST 2010


On Dec 21, 2010, at 6:09 AM, Jacob Bunk Nielsen wrote:

> Hi
> 
> I have noticed that BioPerl does not write OX lines with NCBI TaxIDs in.
> I'd like this feature even though the official way seems to have a a
> source feature with a db_xref to a 'taxon:(\d+)' for this sort of thing.
> 
> I've found and example of an OX line being used for a TaxID at
> ftp://ftp.ebi.ac.uk/pub/databases/embl/cds/README.txt
> 
> Please find attached a patch for reading and writing NCBI TaxIDs to EMBL
> files and a test that verifies that the TaxID will roundtrip being
> written and then read.
> 
> Best regards
> 
> Jacob

Jacob,

Patch was committed:

https://github.com/bioperl/bioperl-live/commit/8b00b61d8641c636ad33e420197b9b7fc452ef42

Thanks for letting us know about this!

chris




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