[Bioperl-l] genbank/embl format ebnf or other formal description

Fields, Christopher J cjfields at illinois.edu
Tue Sep 11 14:39:19 UTC 2012


I think Dan's question is orthogonal to actually parsing a file; it relates more to proper formatting for a particular format based on a specification as well as potential downstream validation.  Bio::SeqIO::genbank is geared for flexibility and can handle a lot of mis-formatted data, it can massage some data into the proper format if needed.  One must recognize the primary driver for the parsers is to get data into objects, not as a format converter (that just happens to be a nice useful side effect).

The problem is, like many formats, a formal specification for Genbank format doesn't exist outside of the NCBI example file (old and incomplete) and the FT definition as far as I know, so calling something 'official' Genbank format isn't possible outside of NCBI.

chris (f)

On Sep 11, 2012, at 9:10 AM, Christopher Bottoms <molecules at cpan.org> wrote:

> Dan,
> Why not use BioPerl's Bio::SeqIO, which can parse GenBank files?
> --Christopher Bottoms
> On Fri, Sep 7, 2012 at 10:43 PM, Dan Kortschak
> <dan.kortschak at adelaide.edu.au> wrote:
>> Thanks Chris. That's remarkable, so many words and not an actual formal
>> specification. I guess I have some work ahead of me. I found the
>> example, but examples rarely contain all edges and corners.
>> Dan
>> On Sat, 2012-09-08 at 03:39 +0000, Fields, Christopher J wrote:
>>> Re: Genbank, the only know specification I know of is for the feature
>>> table portion of the format as you have below.  They do have a
>>> (possibly out of date) example file, note it isn't easily found unless
>>> you search for it:
>>>    http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord
>>> EMBL is better in this regard:
>>>    http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
>>> Note that UniProt Knowledgebase also has a user manual outlining the
>>> similarities and differences with EMBL:
>>>    http://web.expasy.org/docs/userman.html
>>> chris
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