Hi BioStar people,
Here I go again in my odyssey to master EnsEBML. After learning how to use the API and the site, I'm facing difficulties to parse site-generated flatfiles. Tried BioPerl and BioPython without sucess. A common error from python, just to illustrate:
/usr/local/lib/python2.6/dist-packages/Bio/GenBank/Scanner.py:950: UserWarning: Malformed LOCUS line found - is this correct? LOCUS 11 7208 bp DNA HTG 25-MAR-2011
If I edit LOCUS by hand, other parsing errors appear elsewhere. Am I wrong supposing that these EnsEMBL flatfiles are Bio* parseable? My biopython was compiled from the last source version and my Bioperl came from a ubuntu package.