[Biopython] Error parsing EMBL file

[Peter Cock]

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