[Biopython-dev] Parsing malformed genbank files (e.g. VectorNTI)

[Peter]

Tim wrote:
> I have attached two representative example genbank outputs from
> VectorNTI. I don't know if the mailing list accepts attachments, but
> if it can't, is there a place where I can put it (maybe the biopython
> wiki?)

I got them, thanks.  For future reference, it would have been better
to have filed a bug on bugzilla, and then (once the bug is filed) you
can attach files to it.

Earlier Tim wrote:
>>> The current biopython GenBank parser dies while parsing VectorNTI
>>> generated files.  For example, until recently, BioPython did not
>>> accept an empty SOURCE field. It still does not handle an empty
>>> VERSION or ACCESSION fields (consumer.data.id never gets filled),
>>> which is the default for user generated vector maps via VectorNTI.

Now that I've got your two files, my copy of Biopython seem to read
them just fine.  What exactly do you mean by the "parser dies"?  Could
you show us a snippet of code and if relevant the exception error -
plus details of your OS, version of Python and Biopthon etc?

Thanks

Peter