[BioPython] Cannot parse/convert embl formatted files

Peter biopython at maubp.freeserve.co.uk
Sat Aug 12 08:16:19 UTC 2006


I'm not very familiar with the FormatIO system, so I'm not sure what
to suggest there.

 >In principle, I do need to convert the file, what I really need is
> a parser from EMBL formatted data from
> ftp://bighost.ba.itb.cnr.it/pub/Embnet/Database/UTR/data/
> to parse out record with some feature. As I do not see an EMBL
> parser in the Bio package I believe it is not available, right?

You are right, there is currently no BioPython EMBL parser included in
BioPython (other than whatever FormatIO can be persuaded to do on a
good day).  However, it is something that the developers would like to
address (there has been some recent discussion on the mailing list
about sequence input/output in general).

Can you download the same data in GenBank format from another source
like the NCBI instead?

Peter



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