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

Jacob Bunk Nielsen bunk at novozymes.com
Tue Dec 21 07:09:32 EST 2010


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
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