[Biopython-dev] CONTIG records in GenBank files

[Iddo Friedberg]

Not yet, been traveling. Sorry. Will try to get to it next week (plenty of
time on the plane to Stockholm)

Iddo Friedberg, Ph.D.
http://iddo-friedberg.net/contact.html

On Jun 18, 2009 7:10 AM, "Peter" <biopython at maubp.freeserve.co.uk> wrote:

A couple of weeks ago, we were talking about a problem with CONTIG
lines in GenBank files,
http://lists.open-bio.org/pipermail/biopython-dev/2009-June/006192.html

On Sun, Jun 7, 2009 at 10:31 PM, Peter<biopython at maubp.freeserve.co.uk>
wrote:
> On 6/7/09, Iddo Friedberg <idoerg at gmail.com> wrote:
>> Here is the stack dump, coming from the file:
>>
>> ftp://ftp.ncbi.nih.gov/genbank/gbcon11.seq.gz
>> ...
>> Traceback (most recent call last):
>> ...
>> Bio.GenBank.LocationParserError:
>> ...
>
> That looks like Bug 2745 to me - does the patch on that bug work for
> you, and would you be happy storing the CONTIG line as string?

Iddo,

Did you have a chance to try the patch on Bug 2745 yet?
http://bugzilla.open-bio.org/show_bug.cgi?id=2745

If you are happy with the proposed solution, I'd like to get that checked
in...

Thanks,

Peter