[Bioperl-l] Memory requirements for conversion from embl to genbank

Chris Fields cjfields at uiuc.edu
Thu Aug 31 16:57:21 EDT 2006


> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=21727885
> >
> > LOCUS       GVI428955               8027 bp    mRNA    linear   VRL 15-
> APR-2005
> > DEFINITION  Hepatitis GB virus B subgenomic replicon neoRepB.
....

> > The above official GenBank record cannot be parsed and the parsing code
> > silently leaks through and exits with no data written out. I have filed
> > bug #2087.
> 
> No, that was my fault, I forgot to say the input is in genbank format.
> Instead,
> bioperl expected embl code and silently run through. Not nice, still.
> When correctly setting the input format as genbank and output as embl
> I got some record in EMBL record out, but the second 'OS' line with second
> organism is missing. Haven't inspected by diff(1) all the differences.
> Certainly nice testcases - to convert from EMBL to GenaBank and back to
> EMBL
> and use diff to see what happened.
> 
> m.

This is now fixed in CVS.  There actually was a statement in SeqIO::embl
that catches this but a return statement was placed directly before it; not
good.

Chris




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