[Bioperl-l] Memory requirements for conversion from embl to genbank
cjfields at uiuc.edu
Thu Aug 31 16:57:21 EDT 2006
> > LOCUS GVI428955 8027 bp mRNA linear VRL 15-
> > 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.
> 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
> and use diff to see what happened.
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
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