[Biopython] Error parsing EMBL file

[Nick Semenkovich]

Awesome -- works great! (virtualenv makes this so easy!)

Thanks for the quick patch!
- Nick

On Mon, Sep 17, 2012 at 12:31 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Mon, Sep 17, 2012 at 6:22 PM, Nick Semenkovich <semenko at alum.mit.edu> wrote:
>> Looks like it's dying at a line-wrapped location string:
>>
>> RN   [16]
>> RP   1-5181,6229-11775,13275-15420,18210-23250,29410-32271,34850-38580,
>> RP   41454-41724
>> RX   DOI; 10.1128/JB.185.4.1475-1477.2003.
>> RX   PUBMED; 12562822.
>> RA   Pedulla M.L., Ford M.E., Karthikeyan T., Houtz J.M., Hendrix R.W.,
>> RA   Hatfull G.F., Poteete A.R., Gilcrease E.B., Winn-Stapley D.A.,
>> RA   Casjens S.R.;
>> RT   "Corrected sequence of the bacteriophage p22 genome";
>> RL   J. Bacteriol. 185(4):1475-1477(2003).
>>
>>
>> This works if RP is just one line:
>> RP   1-5181,6229-11775,13275-15420,18210-23250,29410-32271,34850-38580,41454-41724
>
> Good detective work :)
>
> Can you try with this fix?
> https://github.com/biopython/biopython/commit/0da9d7e72a95fe788c7c32c9cbc2ac95d84bb7b7
>
> If you installed from source, the easiest way would be to grab the latest
> code from git and reinstall.
>
> If you installed from a package, perhaps you might prefer to manually
> hack the file to make the one line change by hand? Back it up first ;)
> /usr/lib/pymodules/python2.7/Bio/GenBank/Scanner.py
>
> Peter



-- 
Nick Semenkovich
Laboratory of Dr. Jeffrey I. Gordon
Medical Scientist Training Program
School of Medicine
Washington University in St. Louis
314.362.3963 (Lab)
http://web.mit.edu/semenko/